Hydrologic influences on stream temperatures for Little Creek and Scotts Creek, Santa Cruz County, California

Treesearch

Justin M. Louen; Christopher G. Surfleet

2017-01-01

Stream temperature impacts have resulted in increased restrictions on land management, such as timber harvest and riparian restoration, creating considerable uncertainty for future planning and management of redwood (Sequoia sempervirens (D.Don) Endl.) forestlands. Challenges remain in the assessment of downstream cumulative stream...

Library Information-Processing System

NASA Technical Reports Server (NTRS)

1985-01-01

System works with Library of Congress MARC II format. System composed of subsystems that provide wide range of library informationprocessing capabilities. Format is American National Standards Institute (ANSI) format for machine-readable bibliographic data. Adaptable to any medium-to-large library.

VizieR Online Data Catalog: Radial velocity monitoring of 5 FGK stars (Endl+, 2016)

NASA Astrophysics Data System (ADS)

Endl, M.; Brugamyer, E. J.; Cochran, W. D.; MacQueen, P. J.; Robertson, P.; Meschiari, S.; Ramirez, I.; Shetrone, M.; Gullikson, K.; Johnson, M. C.; Wittenmyer, R.; Horner, J.; Ciardi, D. R.; Horch, E.; Simon, A. E.; Howell, S. B.; Everett, M.; Caldwell, C.; Castanheira, B. G.

2016-04-01

Our radial velocity (RV) measurements were obtained using the 2.7m Harlan J. Smith Telescope (HJST; R=60000, 3750-10200Å). For HD 95872, we also obtained 10 precise RV measurements using the 10m Keck I and its HIRES spectrograph (R=50000). (6 data files).

Understanding Sequoia sempervirens

Treesearch

Emily E. Burns

2017-01-01

Humans have no doubt observed the coast redwood, Sequoia sempervirens (D. Don) Endl., in wonder for thousands of years. It is no small task to seek understanding of a species whose sheer size cannot readily be assessed from the ground and whose generation time can exceed that of humans by 100 times. Fortunately, the scientific method has provided a...

Expanding the network of crossdated tree-ring chronologies for Sequoia sempervirens

Treesearch

Allyson L. Carroll; Stephen C. Sillett; Ethan J. Coonen; Benjamin G. Iberle

2017-01-01

Crossdated tree-ring chronologies for the Arcata Community Forest (ACF) and Muir Woods National Monument (Muir Woods) expand the spatial coverage of dated coast redwood (Sequoia sempervirens (D. Don) Endl.) series. Crossdating relies on the common pattern of ring-width variation among tree populations, and dated chronologies have many applications...

Humboldt marten denning ecology in a managed redwood-dominated forest landscape

Treesearch

Desiree A. Early; Keith A. Hamm; Lowell V. Diller; Keith M. Slauson; William J. Zielinski

2017-01-01

The Humboldt marten (Martes caurina humboldtensis) historically occurred in California’s coastal redwood (Sequoia sempervirens (D. Don) Endl.)-dominated forests from northern Sonoma County, California to the Oregon border. The subspecies was thought to be extirpated due to over-trapping and loss of habitat until a...

Redwood seedling responses to light patterns and intensities

Treesearch

Ronald W. Boldenow; Joe R. McBride

2017-01-01

Coast redwood (Sequoia sempervirens (D. Don) Endl.) seedlings were grown from seed in controlled environments with 16 hour photoperiods using three light patterns that mimicked full shade (constant light level), intermittent high light such as long duration sun flecks (low light with 15 minutes of intense light every 2 hours), and large...

Predicting redwood productivity using biophysical data, spatial statistics and site quality indices

Treesearch

John-Pascal Berrill; Kevin L. O’Hara; Shawn Headley

2017-01-01

Coast redwood (Sequoia sempervirens (D. Don) Endl.) height growth and basal area growth are sensitive to variations in site quality. Site factors known to be correlated with redwood stand growth and yield include topographic variables such as position on slope, exposure, and the composite variable: topographic relative moisture index. Species...

The navel orangeworm, Amyelois transtilla (Walker) (Lepidoptera: Pyralidae) discovered in northeastern Mexico feeding on Sapindaceae

USDA-ARS?s Scientific Manuscript database

Amyelois transitella (Walker) (Lepidoptera: Pyralidae), the navel orangeworm, is an important pest of a wide variety fruits and their seeds. We discovered and report for the first time A. transitella feeding on Sapindaceae in wild populations of U. speciosa (Endl.) in northeastern Mexico. We provid...

On the variation of inventory estimates for redwood stands

Treesearch

Daniel Opalach

2017-01-01

There is a tremendous amount of variation in the second growth redwood (Sequoia sempervirens (D. Don) Endl.) forests found along the North Coast of California. In order to make prudent management decisions about these forests, foresters and other resource professionals often conduct timber cruises to collect information on tree species, diameters,...

Management practices eelated to the Restoration of old dorest characteristics in coast redwood forests

Treesearch

Gregory A. Guisti

2012-01-01

A standardized, interactive, interview process was used with practicing Registered Professional Foresters asking a suite of questions to ascertain their management approaches to coast redwood (Sequoia sempervirens [D. Don] Endl.) stands that could best be transferred to other projects and lands interested in recruiting older forest...

Black bear (Ursus americanus Pallas) feeding damage across timber harvest edges in northern California coast redwood (Sequoia sempervirens[D. Don] Endl.) forests, USA

USGS Publications Warehouse

Russell, W.H.; Carnell, K.; McBride, J.R.

2001-01-01

Feeding damage to trees by black bears (Ursus americanus Pallas) was recorded in proximity to timber harvest edges in harvested and old-growth stands of coast redwood (Sequoia sempervirens [D. Don] Endl.) in northern California, USA. Bears exhibited distinct preference in their feeding patterns related to stand structure and composition and to distance from the timber-harvest edge. Most damage was recorded within regenerating stands. Regression analysis indicated that density of damaged trees was negatively correlated with distance from timber harvest edges within old-growth stands. A significant negative correlation was also found between the density of trees damaged by bears and habitat diversity (H') as measured by the Shannon diversity index. In addition, bears exhibited preference for pole-size trees (dbh = 10-50 cm) over all other size classes, and coast redwood over other species. In general, damage by bears appeared to act as a natural thinning agent in even-aged stands. No damage was recorded in old-growth stands except in close proximity to the timber-harvest edge where subcanopy recruitment was high.

Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl

PubMed Central

2010-01-01

Background Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don) Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Results Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2), glycine-rich RNA-binding protein (RNP), and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK) was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Conclusion Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens. PMID:21143964

Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl.

PubMed

Chang, Ing-Feng; Chen, Peng-Jen; Shen, Chin-Hui; Hsieh, Tsung-Ju; Hsu, Ya-Wen; Huang, Bau-Lian; Kuo, Ching-I; Chen, Yu-Ting; Chu, Hsiu-An; Yeh, Kai-Wun; Huang, Li-Chun

2010-12-10

Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don) Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2), glycine-rich RNA-binding protein (RNP), and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK) was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens.

Forest restoration at Redwood National Park: exploring prescribed fire alternatives to second-growth management: a case study

Treesearch

Eamon Engber; Jason Teraoka; Phil van Mantgem

2017-01-01

Almost half of Redwood National Park is comprised of second-growth forests characterized by high stand density, deficient redwood composition, and low understory biodiversity. Typical structure of young redwood stands impedes the recovery of old-growth conditions, such as dominance of redwood (Sequoia sempervirens (D. Don) Endl.), distinct...

Physiology and growth of redwood and Douglas-fir planted after variable density retention outside redwood’s range

Treesearch

Lucy Kerhoulas; Nicholas Kerhoulas; Wade Polda; John-Pascal Berrill

2017-01-01

Reforestation following timber harvests is an important topic throughout the coast redwood (Sequoia sempervirens (D. Don) Endl.) range. Furthermore, as drought-induced mortality spreads across many of California’s forests, it is important to understand how physiology and stand structure influence reforestation success. Finally, as climate...

Coast redwood seedling regeneration following fire in a southern coast redwood forest

Treesearch

Rachel Lazzeri-Aerts; Will Russell

2017-01-01

It has been hypothesized that individuals adapted to conditions near the species’ range edge, may increase the likelihood that the species will persevere under changing climatic conditions (Rehm et al. 2015). The southern coast redwood (Sequoia sempervirens (D. Don) Endl.) forests vary from more northern redwood forests in terms of stand...

A GIS approach to identifying the distribution and structure of coast redwood across its range

Treesearch

Peter Cowan; Emily E. Burns; Richard Campbell

2017-01-01

To better understand the distribution and current structure of coast redwood (Sequoia sempervirens (D.Don) Endl.) forests throughout the range and how it varies by land ownerships, the Save the Redwoods League has conducted a redwood specific analysis of a high resolution forest structure database encompassing the entire natural coast redwood range...

Adaptation to climate change? Moving coast redwood seedlings northward and inland

Treesearch

Christa M. Dagley; John-Pascal Berrill; Forrest T. Johnson; Lucy P. Kerhoulas

2017-01-01

Insight into genetic variation in trees may provide opportunities to select for genotypes that are better adapted to new locations and future climate conditions. We established a field test at two sites in Humboldt County, California to study the performance of coast redwood (Sequoia sempervirens (D. Don) Endl.) under assisted migration. Both test...

Comparing growth and form of coast redwood selfs and outcrosses

Treesearch

John-Pascal Berrill; William J. Libby

2017-01-01

We now report 22 years of new data and observations from the third of three small projects evaluating the effects of inbreeding in coast redwood (Sequoia sempervirens (D. Don) Endl.). We also briefly summarize previously-reported effects of inbreeding on redwood’s cone production, seed set, germination percentage, nursery growth and survival,...

Ninety-two years of tree growth and death in a second-growth redwood forest

Treesearch

Benjamin G. Iberle; Stephen C. Sillett; Robert Van Pelt; Mark Andre

2017-01-01

Mature second-growth redwood (Sequoia sempervirens (D. Don) Endl.) forests are an important and uncommon resource in the redwood region. Development of second-growth redwood forests beyond rotation age is not well understood. Continuous long-term data are especially lacking, considering that the maximum possible age of second-growth stands is now...

Impacts on soils and residual trees from cut-to-length thinning operations in California's redwood forests

Treesearch

Kyungrok Hwang; Han-sup Han; Susan E. Marshall; Deborah S. Page-Dumroese

2017-01-01

Cut-to-length (CTL) harvest systems have recently been introduced for thinning third-growth, young (<25 years old) redwood forests (Sequoia sempervirens (Lamb. ex D. Don) Endl.) in northern California. This type of harvesting can effective for thinning overstocked stands consisting of small-diameter trees. However, forestland managers and government agencies...

Remote camera monitoring and a mark – recapture study of the wandering salamander in a redwood forest canopy

Treesearch

Jim Campbell-Spickler; Stephen C. Sillett

2017-01-01

Crowns of old redwoods (Sequoia sempervirens (D. Don) Endl.) are teaming with life. Storm damage followed by recovery via trunk reiteration increases the structural complexity of redwood crowns over time. Bark and wood surfaces within complex redwood crowns accumulate debris and become covered with epiphytes. Arboreal soils develop beneath...

Cost Differentials between E-Books and Print in Academic Libraries

ERIC Educational Resources Information Center

Bailey, Timothy P.; Scott, Amanda L.; Best, Rickey D.

2015-01-01

Academic libraries continue to face funding pressures compounded by the need to provide students with access to electronic resources, both in journal and book formats. With space constraints and the need to repurpose library space to other uses, libraries must carefully examine the move to e-only formats for books to determine if the format makes…

The listing of coast redwood as endangered under the IUCN red list: lessons for conservation

Treesearch

Erin Clover Kelly

2017-01-01

In 2013, redwood (Sequoia sempervirens (D.Don) Endl.) was listed as endangered under the International Union of Conservation of Nature (IUCN) Red List. While this listing has no political or legal consequences for the management of redwood, it could have economic consequences as land and mill owners of the redwood region have sought to link redwood...

The enigmatic fire regime of coast redwood forests and why it matters

Treesearch

J. Morgan Varner; Erik S. Jules

2017-01-01

Of perhaps all forests in North America, the fire regime of coast redwoods (Sequoia sempervirens (D. Don) Endl.) is most enigmatic. Widely considered a temperate rainforest, a large number of fire history studies depict a forest dominated by frequent surface fire regimes. Coast redwood also has a long list of traits that allow it to persist and...

Ecosystem responses to variable-density thinning for forest restoration in Mill Creek

Treesearch

Lathrop P. Leonard; John-Pascal Berrill; Christa M. Dagley

2017-01-01

Variable-density thinning (VDT) has promise as a forest restoration tool that accelerates development of old-growth redwood (Sequoia sempervirens (D.Don) Endl.) forest characteristics (O’Hara et al. 2010) but can lead to bear damage in north coastal California (Hosack and Fulgham 1998, Perry et al. 2016). Three novel VDT prescriptions (O’...

Tree size, growth, and anatomical factors associated with bear damage in young coast redwood

Treesearch

John-Pascal Berrill; David W. Perry; Larry W. Breshears; Garrett E. Gradillas

2017-01-01

Precommercial thinning is an important tool for coast redwood (Sequoia sempervirens (D Don) Endl.) forest management but is often followed by black bear (Ursus americanus) damage in northern parts of redwood’s natural range (Fritz 1951; Giusti 1988, 1990; Hosack and Fulgham 1998). The bears scrape off bark and feed on the sugar...

A comparison of stand structure and composition following selective-harvest at Byrne-Milliron Forest

Treesearch

Amy K. Petersen; Will Russell

2017-01-01

The effects of selective-harvest on forest composition and structure in the southern range of the coast redwood (Sequoia sempervirens (D. Don) Endl.) forest have not been well documented. This case study focused on the Byrne-Milliron Forest in Santa Cruz County, California where selective-harvest is currently the primary method of timber extraction...

Black bear damage to northwestern conifers in California: a review

Treesearch

Kenneth O. Fulgham; Dennis Hosack

2017-01-01

A total of 789 black bear damaged trees were investigate over a multi-year period on 14 different study sites chosen on lands of four participating timber companies. The sites ranged from 30 to 50 years of age. Four different conifer species were found to have black bear damage: coastal redwood (Sequoia sempervirens (D. Don) Endl.), Douglas-fir (...

[Agronomical and bromatological studies in jicama (Polymnia sonchifolia Poep et Endl.)].

PubMed

Nieto, C

1991-06-01

An analysis of tuber roots yield and nutritional characteristics for 10 lines of jícama (Polymnia sonchifolia Poepp et Endl.) was carried out under the environmental conditions of Santa Catalina Experimental Station (12 degrees C of temperature and 3,100 m above sea level). The following average mean values were obtained: A fresh tuber root's yield from 29,755 to 73,558 kg/ha with 41,547 kg/ha of average, while the yield of the useful part (roots without skin) was from 24,309 to 60,097 kg/ha with 33,944 kg/ha of average. On the other hand, average mean values of 3.7% of protein, 3.5% ashes, 1.5% fat, 3.4% fiber, 2.2% potassium, 0.12% phosphorus, 96 micrograms/100 g iron, and 390 micrograms/100 g zinc, were obtained from the edible root samples. Besides, we obtained average values of 2.47, 2.12, 1.63 and 2.51 g/100 g of fructose, alfa glucose, beta glucose and saccharose, respectively, on edible root samples with skin, for the 10 lines studied. All these analyses were reported on a dry basis.

Effects of the pollution by petroleum on the tracheids along the stem of Podocarpus lambertii Klotzsch ex Endl., Podocarpaceae.

PubMed

Maranho, L T; Dziedzic, M; Muñiz, G I B; Kuniyoshi, Y S; Galvão, F

2009-05-01

Podocarpus lambertii Klotzsch ex Endl. (Podocarpaceae) is native and a member of the Pinophyta (Gymnosperm) of southern Brazil, locally known as 'pinheiro-bravo'. The present work aims to investigate the effects of petroleum on the tracheids dimensions. Wood samples from twenty individuals were studied along the stem, ten being exposed to pollution and ten used as a control set. The wood samples were collected from incisions at three levels: at the ground level, and one and two metres above the ground level. From these samples, sub-samples were selected at the border of the growth layers in the vascular cambium-medulla direction. The methodology followed that traditionally recommended for plant anatomy studies, with analyses done by light microscopy (OLYMPUS - BX41) assisted by the software Image Pro-plus for measurements. Comparison of the individuals exposed to petroleum with the control set, showed that the length, diameter and cell wall width of the tracheids of the former were smaller, a trend which was statistically significant according to the Student's t-test. These traits were observed mainly on the tracheids of the last growth layer, corresponding to the year in which the individuals were exposed to petroleum.

Satisfaction Formation Processes in Library Users: Understanding Multisource Effects

ERIC Educational Resources Information Center

Shi, Xi; Holahan, Patricia J.; Jurkat, M. Peter

2004-01-01

This study explores whether disconfirmation theory can explain satisfaction formation processes in library users. Both library users' needs and expectations are investigated as disconfirmation standards. Overall library user satisfaction is predicted to be a function of two independent sources--satisfaction with the information product received…

Cone production, seed dispersal, germination in...old-growth redwood cut and uncut stands

Treesearch

Kenneth N. Boe

1968-01-01

Records of 5 and 6 years' cone crops in old-growth redwood (Sequoia sempervirens [D. Don Endl.] stands in northern California were studied for silvical facts. They show that (a) the principal trees in both cut and uncut stands bore fair to good cone crops for 5 consecutive years, (b) maximum seed dispersal of both total and sound seed occurred in winter, (c)...

Content of polyphenolic compounds in the Nigerian stimulants Cola nitida ssp. alba, Cola nitida ssp. rubra A. Chev, and Cola acuminata Schott & Endl and their antioxidant capacity.

PubMed

Atawodi, Sunday Ene-Ojo; Pfundstein, Beate; Haubner, Roswitha; Spiegelhalder, Bertold; Bartsch, Helmut; Owen, Robert Wyn

2007-11-28

Varieties of kola nuts (Cola nitida alba, Cola nitida rubra A. Chev, and Cola acuminata Schott & Endl), a group of popular Nigerian and West African stimulants, were analyzed for their content of secondary plant metabolites. The three varieties of the kola nuts contained appreciable levels of (+)-catechin (27-37 g/kg), caffeine (18-24 g/kg), (-)-epicatechin (20-21 g/kg), procyanidin B 1 [epicatechin-(4beta-->8)-catechin] (15-19 g/kg), and procyanidin B2 [epicatechin-(4beta-->8)-epicatechin] (7-10 g/kg). Antioxidant capacity of the extracts and purified metabolites was assessed by two HPLC-based and two colorimetric in vitro assays. Extracts of all varieties exhibited antioxidant capacity with IC 50 values in the range 1.70-2.83 and 2.74-4.08 mg/mL in the hypoxanthine/xanthine oxidase and 2-deoxyguanosine HPLC-based assays, respectively. Utilization of HPLC-based assays designed to reflect in situ generation of free radicals (e.g., HO(*)), as opposed to general assays (DPPH, FRAP) in common use which do not, indicate that, of the major secondary plant metabolites present in kola nut extracts, caffeine is potentially the more effective cancer chemopreventive metabolite in terms of its antioxidant capacity.

Nuclide radioactive decay data uncertainties library

NASA Astrophysics Data System (ADS)

Barabanova, D. S.; Zherdev, G. M.

2017-01-01

The results of the developing the library of uncertainties of radioactive decay data in the ABBN data library format are described. Different evaluations of uncertainties were compared and their effects on the results of calculations of residual energy release were determined using the test problems and experiment. Tables were generated in the ABBN format with the data obtained on the basis of libraries in ENDF-6 format. 3821 isotopes from the ENDF/B-7 data library, 3852 isotopes from the JEFF-3.11 data library and 1264 isotopes from the JENDL-4.0 data library were processed. It was revealed that the differences in the evaluations accepted in different decay data libraries are not so big, although they sometimes exceed the uncertainties assigned to the data in the ENDF/B-7 and JEFF-3.11 libraries, which as a rule, they agree with each other. On the basis of developed method it is supposed to create a library of data uncertainties for radioactive decay within the constant data system in FSUE RFNC-VNIIEF with its further connection with CRYSTAL module.

Building Multi-Discipline, Multi-Format Digital Libraries Using Clusters and Buckets. Degree rewarded by Old Dominion Univ. on Aug. 1997

NASA Technical Reports Server (NTRS)

Nelson, Michael L.

1997-01-01

Our objective was to study the feasibility of extending the Dienst protocol to enable a multi-discipline, multi-format digital library. We implemented two new technologies: cluster functionality and publishing buckets. We have designed a possible implementation of clusters and buckets, and have prototyped some aspects of the resultant digital library. Currently, digital libraries are segregated by the disciplines they serve (computer science, aeronautics, etc.), and by the format of their holdings (reports, software, datasets, etc.). NCSTRL+ is a multi-discipline, multi-format digital library (DL) prototype created to explore the feasibility of the design and implementation issues involved with created a unified, canonical scientific and technical information (STI) DL. NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible DL that provides access to over 80 university departments and laboratories. We have extended the Dienst protocol (version 4.1.8), the protocol underlying NCSTRL, to provide the ability to cluster independent collections into a logically centralized DL based upon subject category classification, type of organization, and genre of material. The concept of buckets provides a mechanism for publishing and managing logically linked entities with multiple data formats.

A rapid and sensitive assay method for measuring amine oxidase based on hydrogen peroxide-titanium complex formation.

PubMed

Nag; Saha; Choudhuri

2000-08-22

Hydrogenperoxide (H(2)O(2)) is an end product of diamine and polyamine oxidation by their respective oxidase enzymes. A new sensitive assay method is based on a H(2)O(2)-titanium (Ti) complex formation as an indicator of H(2)O(2) production due to polyamine oxidation. The orange-yellow coloured H(2)O(2)-Ti complex was measured at 410 nm in a Shimadzu spectrophotometer. The assay conditions for maximum diamine oxidase (DAO) and polyamine oxidase (PAO) as standardized here using the hypocotyl tissues of Vigna catjang Endl. cv Pusa Barsati consisted of pH 7.4 (40 mM potassium phosphate buffer), 3 mM substrate (putrescine or spermine), 37 degrees C incubation temperature and 30 min incubation time in the presence of catechol (10(-2) M) used as an inhibitor of both peroxidase and catalase activity. The method described here was significantly more sensitive than the starch-iodide method [T.A. Smith, Biochem. Biophys. Res. Commun. 41 (1970) 1452-1456], which could be improved further if measured under the same assay conditions as described for the H(2)O(2)-Ti method. Sensitivity of the present method was tested by assaying DAO/PAO activity in auxin treated hypocotyls of Vigna and comparing it with the starch-iodide method in two other plant samples.

Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique.

PubMed

Toral Ibañez, Manuel; Caru, Margarita; Herrera, Miguel A; Gonzalez, Luis; Martin, Luis M; Miranda, Jorge; Navarro-Cerrillo, Rafael M

2009-02-01

A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D. Don) Endl. in Chile. Ten (out of 34) clones from introduction trial located in Voipir-Villarrica, Chile, were studied. The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction. The PCR tests were carried out employing 10-mer random primers. The amplification products were detected by electrophoresis in agarose gels. Forty nine polymorphic bands were obtained with the selected primers (BG04, BF07, BF12, BF13, and BF14) and were ordered according to their molecular size. The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA). Of the primers tested, 5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism. A total of 49 polymorphic RAPD bands were detected out of 252 bands. The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones, suggesting a geographic relationship. The results indicate that the RAPD markers permitted the identification of the assayed clones, although they are derived from the same geographic origin.

Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique*

PubMed Central

Toral Ibañez, Manuel; Caru, Margarita; Herrera, Miguel A.; Gonzalez, Luis; Martin, Luis M.; Miranda, Jorge; Navarro-Cerrillo, Rafael M.

2009-01-01

A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D. Don) Endl. in Chile. Ten (out of 34) clones from introduction trial located in Voipir-Villarrica, Chile, were studied. The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction. The PCR tests were carried out employing 10-mer random primers. The amplification products were detected by electrophoresis in agarose gels. Forty nine polymorphic bands were obtained with the selected primers (BG04, BF07, BF12, BF13, and BF14) and were ordered according to their molecular size. The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA). Of the primers tested, 5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism. A total of 49 polymorphic RAPD bands were detected out of 252 bands. The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones, suggesting a geographic relationship. The results indicate that the RAPD markers permitted the identification of the assayed clones, although they are derived from the same geographic origin. PMID:19235269

The Nonsubscription Side of Periodicals: Changes in Library Operations and Costs between Print and Electronic Formats

ERIC Educational Resources Information Center

Schonfeld, Roger C.; King, Donald W.; Okerson, Ann; Fenton, Eileen Gifford

2004-01-01

Many academic and research libraries are in the midst of what may ultimately be a major transition for various parts of their collection--a shift from print to electronic format. Libraries that had long subscribed only to print versions of journals are, in increasing numbers, licensing electronic versions to replace the print. What effects will…

Simple Ontology Format (SOFT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sorokine, Alexandre

2011-10-01

Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

The USF Libraries Virtual Library Project: A Blueprint for Development.

ERIC Educational Resources Information Center

Metz-Wiseman, Monica; Silver, Susan; Hanson, Ardis; Johnston, Judy; Grohs, Kim; Neville, Tina; Sanchez, Ed; Gray, Carolyn

This report of the Virtual Library Planning Committee (VLPC) is intending to serve as a blueprint for the University of South Florida (USF) Libraries as it shifts from print to digital formats in its evolution into a "Virtual Library". A comprehensive planning process is essential for the USF Libraries to make optimum use of technology,…

Java Library for Input and Output of Image Data and Metadata

NASA Technical Reports Server (NTRS)

Deen, Robert; Levoe, Steven

2003-01-01

A Java-language library supports input and output (I/O) of image data and metadata (label data) in the format of the Video Image Communication and Retrieval (VICAR) image-processing software and in several similar formats, including a subset of the Planetary Data System (PDS) image file format. The library does the following: It provides low-level, direct access layer, enabling an application subprogram to read and write specific image files, lines, or pixels, and manipulate metadata directly. Two coding/decoding subprograms ("codecs" for short) based on the Java Advanced Imaging (JAI) software provide access to VICAR and PDS images in a file-format-independent manner. The VICAR and PDS codecs enable any program that conforms to the specification of the JAI codec to use VICAR or PDS images automatically, without specific knowledge of the VICAR or PDS format. The library also includes Image I/O plugin subprograms for VICAR and PDS formats. Application programs that conform to the Image I/O specification of Java version 1.4 can utilize any image format for which such a plug-in subprogram exists, without specific knowledge of the format itself. Like the aforementioned codecs, the VICAR and PDS Image I/O plug-in subprograms support reading and writing of metadata.

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

PubMed

Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

2016-01-01

For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

Production and testing of the ENEA-Bologna VITJEFF32.BOLIB (JEFF-3.2) multi-group (199 n + 42 γ) cross section library in AMPX format for nuclear fission applications

NASA Astrophysics Data System (ADS)

Pescarini, Massimo; Orsi, Roberto; Frisoni, Manuela

2017-09-01

The ENEA-Bologna Nuclear Data Group produced the VITJEFF32.BOLIB multi-group coupled neutron/photon (199 n + 42 γ) cross section library in AMPX format, based on the OECD-NEA Data Bank JEFF-3.2 evaluated nuclear data library. VITJEFF32.BOLIB was conceived for nuclear fission applications as European counterpart of the ORNL VITAMIN-B7 similar library (ENDF/B-VII.0 data). VITJEFF32.BOLIB has the same neutron and photon energy group structure as the former ORNL VITAMIN-B6 reference library (ENDF/B-VI.3 data) and was produced using similar data processing methodologies, based on the LANL NJOY-2012.53 nuclear data processing system for the generation of the nuclide cross section data files in GENDF format. Then the ENEA-Bologna 2007 Revision of the ORNL SCAMPI nuclear data processing system was used for the conversion into the AMPX format. VITJEFF32.BOLIB contains processed cross section data files for 190 nuclides, obtained through the Bondarenko (f-factor) method for the treatment of neutron resonance self-shielding and temperature effects. Collapsed working libraries of self-shielded cross sections in FIDO-ANISN format, used by the deterministic transport codes of the ORNL DOORS system, can be generated from VITJEFF32.BOLIB through the cited SCAMPI version. This paper describes the methodology and specifications of the data processing performed and presents some results of the VITJEFF32.BOLIB validation.

Introducing ORACLE: Library Processing in a Multi-User Environment.

ERIC Educational Resources Information Center

Queensland Library Board, Brisbane (Australia).

Currently being developed by the State Library of Queensland, Australia, ORACLE (On-Line Retrieval of Acquisitions, Cataloguing, and Circulation Details for Library Enquiries) is a computerized library system designed to provide rapid processing of library materials in a multi-user environment. It is based on the Australian MARC format and fully…

Integrating Resources in the Education Library: Trends, Issues, and Reality

ERIC Educational Resources Information Center

Osa, Justina O.

2005-01-01

Resources found in the typical education library that supports teacher education programs often include print and non-print library items, and other items that are unique to education library collections. This article attempts to share what the education library is doing to integrate all of its resources irrespective of their formats. The main…

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn)

PubMed Central

Yin, Jingjing; Li, Liangjun; Chen, Xuehao

2013-01-01

Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root. PMID:23840598

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.

PubMed

Smelter, Andrey; Astra, Morgan; Moseley, Hunter N B

2017-03-17

The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis. To aid in the use of this public resource, we have developed a package called nmrstarlib in the popular open-source programming language Python. The nmrstarlib's implementation is very efficient, both in design and execution. The library has facilities for reading and writing both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and list-based data structures, making access and manipulation of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records represented as individual Python dictionary data structures). Another major advantage of this design is that data stored in original NMR-STAR can be easily converted into its equivalent JavaScript Object Notation (JSON) format, a lightweight data interchange format, facilitating data access and manipulation using Python and any other programming language that implements a JSON parser/generator (i.e., all popular programming languages). We have also developed tools to visualize assigned chemical shift values and to convert between NMR-STAR and JSONized NMR-STAR formatted files. Full API Reference Documentation, User Guide and Tutorial with code examples are also available. We have tested this new library on all current BMRB entries: 100% of all entries are parsed without any errors for both NMR-STAR version 2.1 and version 3.1 formatted files. We also compared our software to three currently available Python libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR. The nmrstarlib package is a simple, fast, and efficient library for accessing data from the BMRB. The library provides an intuitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files. The nmrstarlib package can be used as a library for accessing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical shift values. Furthermore, the nmrstarlib implementation provides a guide for effectively JSONizing other older scientific formats, improving the FAIRness of data in these formats.

Integrated Online Software for Libraries: An Overview of Today's Best-Selling IOLS. Options from the U.S. Perspective.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Profiles the top-selling IOLS (integrated online library systems) software for libraries based on sales figures reported in the 1996 "Library Journal" annual survey of the library automation marketplace. Highlights include microcomputer-based systems and minicomputer-based systems, system components, MARC formats, and market sectors.…

What Qualifications and Skills Are Important for Digital Librarian Positions in Academic Libraries? A Job Advertisement Analysis

ERIC Educational Resources Information Center

Choi, Youngok; Rasmussen, Edie

2009-01-01

As academic library functions and activities continue to evolve, libraries have broadened the traditional library model, which focuses on management of physical resources and activities, to include a digital library model, transforming resources and services into digital formats to support teaching, learning, and research. This transition has…

Interactive Visualization Systems and Data Integration Methods for Supporting Discovery in Collections of Scientific Information

DTIC Science & Technology

2011-05-01

iTunes illustrate the difference between the centralized approach of digital library systems and the distributed approach of container file formats...metadata in a container file format. Apple’s iTunes uses a centralized metadata approach and allows users to maintain song metadata in a single...one iTunes library to another the metadata must be copied separately or reentered in the new library. This demonstrates the utility of storing metadata

Imaging Technology in Libraries: Photo CD Offers New Possibilities.

ERIC Educational Resources Information Center

Beiser, Karl

1993-01-01

Describes Kodak's Photo CD technology, a format for the storage and retrieval of photographic images in electronic form. Highlights include current and future Photo CD formats; computer imaging technology; ownership issues; hardware for using Photo CD; software; library and information center applications, including image collections and…

PC104 Control Environment Development and Use for Testing the Dynamic Accuracy of the MicroStrain 3DM-GX1 Sensor

DTIC Science & Technology

2007-06-01

Seen here is the actual function code: 92 void SerComInit(void) 93 { 94 out8(sbase + 4, 0x09); // MCR data terminal ready 95...the main function, is the function that will do this: 71 61 StopCONTmode(); The definition of this function is after the main function and...67 { 68 if(checksum==dataid+roll+pitch+yaw+timerticks) 69 { 70 cout<<"Its good data"<<endl; 71

Collaborative Collections Management Programs in ARL Libraries. SPEC Kit 235.

ERIC Educational Resources Information Center

Soete, George J., Comp.

1998-01-01

This survey was conducted to discover how extensively ARL (Association of Research Libraries) libraries are involved in formal, active programs of collaboration for collections management. Seventy ARL libraries completed a questionnaire focusing on all collections formats and a number of related collections management activities. Results indicated…

Creating an Information Literacy Badges Program in Blackboard: A Formative Program Evaluation

ERIC Educational Resources Information Center

Tunon, Johanna; Ramirez, Laura Lucio; Ryckman, Brian; Campbell, Loy; Mlinar, Courtney

2015-01-01

A formative program evaluation using Stufflebeam's (2010) Context, Input, Process, Product (CIPP) model was conducted to assess the use of digital badges for tracking basic library instructional skills across academic programs at Nova Southeastern University. Based on the evaluation of pilot library modules and Blackboard Learn's badges…

ENDF-6 Formats Manual Data Formats and Procedures for the Evaluated Nuclear Data File ENDF/B-VI and ENDF/B-VII

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herman, M.; Members of the Cross Sections Evaluation Working Group

2009-06-01

In December 2006, the Cross Section Evaluation Working Group (CSEWG) of the United States released the new ENDF/B-VII.0 library. This represented considerable achievement as it was the 1st major release since 1990 when ENDF/B-VI has been made publicly available. The two libraries have been released in the same format, ENDF-6, which has been originally developed for the ENDF/B-VI library. In the early stage of work on the VII-th generation of the library CSEWG made important decision to use the same formats. This decision was adopted even though it was argued that it would be timely to modernize the formats andmore » several interesting ideas were proposed. After careful deliberation CSEWG concluded that actual implementation would require considerable resources needed to modify processing codes and to guarantee high quality of the files processed by these codes. In view of this the idea of format modernization has been postponed and ENDF-6 format was adopted for the new ENDF/B-VII library. In several other areas related to ENDF we made our best to move beyond established tradition and achieve maximum modernization. Thus, the 'Big Paper' on ENDF/B-VII.0 has been published, also in December 2006, as the Special Issue of Nuclear Data Sheets 107 (1996) 2931-3060. The new web retrieval and plotting system for ENDF-6 formatted data, Sigma, was developed by the NNDC and released in 2007. Extensive paper has been published on the advanced tool for nuclear reaction data evaluation, EMPIRE, in 2007. This effort was complemented with release of updated set of ENDF checking codes in 2009. As the final item on this list, major revision of ENDF-6 Formats Manual was made. This work started in 2006 and came to fruition in 2009 as documented in the present report.« less

Evaluation of "credit card" libraries for inhibition of HIV-1 gp41 fusogenic core formation.

PubMed

Xu, Yang; Lu, Hong; Kennedy, Jack P; Yan, Xuxia; McAllister, Laura A; Yamamoto, Noboru; Moss, Jason A; Boldt, Grant E; Jiang, Shibo; Janda, Kim D

2006-01-01

Protein-protein interactions are of critical importance in biological systems, and small molecule modulators of such protein recognition and intervention processes are of particular interest. To investigate this area of research, we have synthesized small-molecule libraries that can disrupt a number of biologically relevant protein-protein interactions. These library members are designed upon planar motif, appended with a variety of chemical functions, which we have termed "credit-card" structures. From two of our "credit-card" libraries, a series of molecules were uncovered which act as inhibitors against the HIV-1 gp41 fusogenic 6-helix bundle core formation, viral antigen p24 formation, and cell-cell fusion at low micromolar concentrations. From the high-throughput screening assays we utilized, a selective index (SI) value of 4.2 was uncovered for compound 2261, which bodes well for future structure activity investigations and the design of more potent gp41 inhibitors.

Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

PubMed

Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

2016-08-08

DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

Study on Mass Conservation Techniques for Treatment of Library and Archives Material.

ERIC Educational Resources Information Center

Wachter, Wolfgang, Ed.

This document outlines the present state of development in mass restoration of library and archive materials and relates it to the economic, technical, and aesthetic aspects of various conservation and restoration methods, and discusses their implications for the formation of preservation policies in libraries. Ill effects to library materials…

Books, Bytes, Buildings, and Bodies: Public Libraries in the 21st Century.

ERIC Educational Resources Information Center

Hage, Christine Lind

1999-01-01

Considers the changing roles of public libraries and challenges facing them in the future. Topics include core skills needed by library professionals, print and nonprint materials, the inclusion of new formats, blending traditional and electronic library resources, the expanded roles and responsibilities of librarians, meeting user needs, and…

Library Systems Office Organization. SPEC Kit and SPEC Flyer 211.

ERIC Educational Resources Information Center

Muir, Scott P., Comp.

The roles and responsibilities of the library systems officer continues to change as libraries move beyond the automation of library functions to offering resources in electronic formats and electronic access to information about collections beyond the walls of the home institution. This survey was designed to collect data and document some of the…

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.

PubMed

Shave, Steven; Mann, Stefan; Koszela, Joanna; Kerr, Alastair; Auer, Manfred

2018-01-01

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.

National Library Service of the Library of Congress: New Electronic Information Projects. Part Four of a Four-Part Series.

ERIC Educational Resources Information Center

McNulty, Tom, Ed.

1995-01-01

This final installment of a four-part series on the National Library Service (NLS) examines recently implemented and future projects, with a focus on alternative formats for patrons with disabilities. Discusses LOCIS, the Library of Congress online public access catalog; MARVEL, the Library of Congress gopher; the NLS Web site; and computer disk…

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PubMed Central

Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R.

2015-01-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/. PMID:26037908

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

PubMed

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R

2015-09-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benchmark test of transport calculations of gold and nickel activation with implications for neutron kerma at Hiroshima.

PubMed

Hoshi, M; Hiraoka, M; Hayakawa, N; Sawada, S; Munaka, M; Kuramoto, A; Oka, T; Iwatani, K; Shizuma, K; Hasai, H

1992-11-01

A benchmark test of the Monte Carlo neutron and photon transport code system (MCNP) was performed using a 252Cf fission neutron source to validate the use of the code for the energy spectrum analyses of Hiroshima atomic bomb neutrons. Nuclear data libraries used in the Monte Carlo neutron and photon transport code calculation were ENDF/B-III, ENDF/B-IV, LASL-SUB, and ENDL-73. The neutron moderators used were granite (the main component of which is SiO2, with a small fraction of hydrogen), Newlight [polyethylene with 3.7% boron (natural)], ammonium chloride (NH4Cl), and water (H2O). Each moderator was 65 cm thick. The neutron detectors were gold and nickel foils, which were used to detect thermal and epithermal neutrons (4.9 eV) and fast neutrons (> 0.5 MeV), respectively. Measured activity data from neutron-irradiated gold and nickel foils in these moderators decreased to about 1/1,000th or 1/10,000th, which correspond to about 1,500 m ground distance from the hypocenter in Hiroshima. For both gold and nickel detectors, the measured activities and the calculated values agreed within 10%. The slopes of the depth-yield relations in each moderator, except granite, were similar for neutrons detected by the gold and nickel foils. From the results of these studies, the Monte Carlo neutron and photon transport code was verified to be accurate enough for use with the elements hydrogen, carbon, nitrogen, oxygen, silicon, chlorine, and cadmium, and for the incident 252Cf fission spectrum neutrons.

Three Perspectives on Independent Ebook Adoption in Academic Libraries

ERIC Educational Resources Information Center

Brahme, Maria; Delich, Patricia; Heilman, Elena

2012-01-01

For more than a decade, librarians have struggled to balance making the convenience of the ebook formats available while alleviating users' frustrations with the disparities between the myriad formats. This article tells the story of another area of ebook concern: How can independently published ebooks make it into a library's collections? The…

Virtual Libraries: Meeting the Corporate Challenge.

ERIC Educational Resources Information Center

DiMattia, Susan S.; Blumenstein, Lynn C.

1999-01-01

Discusses virtual libraries in corporate settings from the viewpoint of five special librarians. Highlights include competitive advantage, space and related collection issues, the use of technology, corporate culture, information overload, library vulnerability and downsizing, and the importance of service over format. (LRW)

Handbook of Laws and Regulations Affecting Public Libraries in New York State. Second Edition.

ERIC Educational Resources Information Center

Eisner, Joseph, Comp.

In a looseleaf format which permits easy revision, this handbook synthesizes statutes, opinions, and regulations that affect library operation in New York State. The text consists of excerpts and synopses of statutes and opinions from state agencies and courts. Topics include: (1) library types; (2) establishment and dissolution of libraries; (3)…

The RLG Conspectus: Its Uses and Benefits.

ERIC Educational Resources Information Center

Ferguson, Anthony W.; And Others

1988-01-01

Describes the Research Libraries Group (RLG) conspectus for collection evaluation and how it is being used to foster cooperation among North American libraries. Discussion of the internal benefits includes library planning, collection policy formation, staffing allocation and training, funding allocation and requests, accreditation, faculty…

BUGJEFF311.BOLIB (JEFF-3.1.1) and BUGENDF70.BOLIB (ENDF/B-VII.0) - Generation Methodology and Preliminary Testing of two ENEA-Bologna Group Cross Section Libraries for LWR Shielding and Pressure Vessel Dosimetry

NASA Astrophysics Data System (ADS)

Pescarini, Massimo; Sinitsa, Valentin; Orsi, Roberto; Frisoni, Manuela

2016-02-01

Two broad-group coupled neutron/photon working cross section libraries in FIDO-ANISN format, dedicated to LWR shielding and pressure vessel dosimetry applications, were generated following the methodology recommended by the US ANSI/ANS-6.1.2-1999 (R2009) standard. These libraries, named BUGJEFF311.BOLIB and BUGENDF70.BOLIB, are respectively based on JEFF-3.1.1 and ENDF/B-VII.0 nuclear data and adopt the same broad-group energy structure (47 n + 20 γ) of the ORNL BUGLE-96 similar library. They were respectively obtained from the ENEA-Bologna VITJEFF311.BOLIB and VITENDF70.BOLIB libraries in AMPX format for nuclear fission applications through problem-dependent cross section collapsing with the ENEA-Bologna 2007 revision of the ORNL SCAMPI nuclear data processing system. Both previous libraries are based on the Bondarenko self-shielding factor method and have the same AMPX format and fine-group energy structure (199 n + 42 γ) as the ORNL VITAMIN-B6 similar library from which BUGLE-96 was obtained at ORNL. A synthesis of a preliminary validation of the cited BUGLE-type libraries, performed through 3D fixed source transport calculations with the ORNL TORT-3.2 SN code, is included. The calculations were dedicated to the PCA-Replica 12/13 and VENUS-3 engineering neutron shielding benchmark experiments, specifically conceived to test the accuracy of nuclear data and transport codes in LWR shielding and radiation damage analyses.

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Comparison of WLN, RLIN, and OCLC.

ERIC Educational Resources Information Center

Bolin, Mary K., Ed.

This report examines the costs of and services provided by the three major bibliographic utilities, OCLC (Online Computer Library Center), RLIN (Research Libraries Information Network), and WLN (Western Library Network). The services examined include acquisitions, cataloging, interlibrary loan, and reference. To examine costs, the format of the…

Government documents and the online catalog.

PubMed

Lynch, F H; Lasater, M C

1990-01-01

Prior to planning for implementing the NOTIS system, the Vanderbilt Medical Center Library had not fully cataloged its government publications, and records for these materials were not in machine-readable format. A decision was made that patrons should need to look in only one place for all library materials, including the Health and Human Services Department publications received each year from the central library's Government Documents Unit. Beginning in 1985, these publications were added to the library's database, and the entire 7,200-piece collection is now in the online catalog. Working with these publications has taught the library much about the advantages and disadvantages of cataloging government documents in an online environment. It was found that OCLC cataloging copy is eventually available for most titles, although only about 10% of the records have MeSH headings. Staff time is the major expenditure; problems are caused by documents' irregular nature, frequent format changes, and difficult authority work. Since their addition to the online catalog, documents are used more and the library has better control.

Government documents and the online catalog.

PubMed Central

Lynch, F H; Lasater, M C

1990-01-01

Prior to planning for implementing the NOTIS system, the Vanderbilt Medical Center Library had not fully cataloged its government publications, and records for these materials were not in machine-readable format. A decision was made that patrons should need to look in only one place for all library materials, including the Health and Human Services Department publications received each year from the central library's Government Documents Unit. Beginning in 1985, these publications were added to the library's database, and the entire 7,200-piece collection is now in the online catalog. Working with these publications has taught the library much about the advantages and disadvantages of cataloging government documents in an online environment. It was found that OCLC cataloging copy is eventually available for most titles, although only about 10% of the records have MeSH headings. Staff time is the major expenditure; problems are caused by documents' irregular nature, frequent format changes, and difficult authority work. Since their addition to the online catalog, documents are used more and the library has better control. PMID:2295010

Libraries for People with Handicaps: A Directory of Public Library Resources and Services in Ohio. Second edition.

ERIC Educational Resources Information Center

Ohio State Library, Columbus.

This second edition of the directory contains information collected from 249 public libraries for use by the handicapped, i.e., blind, physically disabled, aged, shut-in, and institutionalized persons. Several changes in format have been made in response to users' reactions to the first edition. For quick reference to library services, materials…

The X6XS. 0 cross section library for MCNP-4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruvost, N.L.; Seamon, R.E.; Rombaugh, C.T.

1991-06-01

This report documents the work done by X-6, HSE-6, and CTR Technical Services to produce a comprehensive working cross-section library for MCNP-4 suitable for SUN workstations and similar environments. The resulting library consists of a total of 436 files (one file for each ZAID). The library is 152 Megabytes in Type 1 format and 32 Megabytes in Type 2 format. Type 2 can be used when porting the library from one computer to another of the same make. Otherwise, Type 1 must be used to ensure portability between different computer systems. Instructions for installing the library and adding ZAIDs tomore » it are included here. Also included is a description of the steps necessary to install and test version 4 of MCNP. To improve readability of this report, certain commands and filenames are given in uppercase letters. The actual command or filename on the SUN workstation, however, must be specified in lowercase letters. Any questions regarding the data contained in the library should be directed to X-6 and any questions regarding the installation of the library and the testing that was performed should be directed to HSE-6. 9 refs., 7 tabs.« less

Evaluation of “Credit Card” Libraries for Inhibition of HIV-1 gp41 Fusogenic Core Formation

PubMed Central

Xu, Yang; Lu, Hong; Kennedy, Jack P.; Yan, Xuxia; McAllister, Laura; Yamamoto, Noboru; Moss, Jason A.; Boldt, Grant E.; Jiang, Shibo; Janda, Kim D.

2008-01-01

Protein-protein interactions are of critical importance in biological systems and small molecule modulators of such protein recognition and intervention processes are of particular interests. To investigate this area of research, we have synthesized small molecule libraries that can disrupt a number of biologically relevant protein-protein interactions. These library members are designed upon planar motifs, appended with a variety of chemical functions, which we have termed as “credit-card” structures. From two of our “credit-card” libraries, a series of molecules were uncovered which act as inhibitors against the HIV-1 gp41 fusogenic 6-helix bundle core formation, viral antigen p24 formation and cell-cell fusion at low micromolar concentrations. From the high-throughput screening assays we utilized, a selective index (SI) value of 4.2 was uncovered for compound 2261, which bodes well for future structure activity investigations and the design of more potent gp41 inhibitors. PMID:16827565

Clinical and academic use of electronic and print books: the Health Sciences Library System e-book study at the University of Pittsburgh.

PubMed

Folb, Barbara L; Wessel, Charles B; Czechowski, Leslie J

2011-07-01

The purpose of the Health Sciences Library System (HSLS) electronic book (e-book) study was to assess use, and factors affecting use, of e-books by all patron groups of an academic health sciences library serving both university and health system-affiliated patrons. A web-based survey was distributed to a random sample (n=5,292) of holders of library remote access passwords. A total of 871 completed and 108 partially completed surveys were received, for an approximate response rate of 16.5%-18.5%, with all user groups represented. Descriptive and chi-square analysis was done using SPSS 17. Library e-books were used by 55.4% of respondents. Use by role varied: 21.3% of faculty reported having assigned all or part of an e-book for class readings, while 86% of interns, residents, and fellows reported using an e-book to support clinical care. Respondents preferred print for textbooks and manuals and electronic format for research protocols, pharmaceutical, and reference books, but indicated high flexibility about format choice. They rated printing and saving e-book content as more important than annotation, highlighting, and bookmarking features. Respondents' willingness to use alternate formats, if convenient, suggests that libraries can selectively reduce title duplication between print and e-books and still support library user information needs, especially if publishers provide features that users want. Marketing and user education may increase use of e-book collections.

Redesigning a library-based genetics class research project through instructional theory and authentic experience.

PubMed

Tennant, Michele R; Edwards, Mary; Miyamoto, Michael M

2012-04-01

How can the library-based research project of a genetics course be reinvigorated and made sustainable without sacrificing educational integrity? The University of Florida's Health Science Center Library provides the case study. Since 1996, the librarian has codeveloped, supported, and graded all components of the project. In 2009, the project evolved from a single-authored paper to a group-work poster, with graded presentations hosted by the library. In 2010, students were surveyed regarding class enhancements. Responses indicated a preference for collaborative work and the poster format and suggested the changes facilitated learning. Instructors reported that the poster format more clearly documented students' understanding of genetics. Results suggest project enhancements contributed to greater appreciation, understanding, and application of classroom material and offered a unique and authentic learning experience, without compromising educational integrity. The library benefitted through increased visibility as a partner in the educational mission and development of a sustainable instructional collaboration.

Neutron Fission of 235,237,239U and 241,243Pu: Cross Sections, Integral Cross Sections and Cross Sections on Excited States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Younes, W; Britt, H C

In a recent paper submitted to Phys. Rev. C they have presented estimates for (n,f) cross sections on a series of Thorium, Uranium and Plutonium isotopes over the range E{sub n} = 0.1-2.5 MeV. The (n,f) cross sections for many of these isotopes are difficult or impossible to measure in the laboratory. The cross sections were obtained from previous (t,pf) reaction data invoking a model which takes into account the differences between (t,pf) and (n,f) reaction processes, and which includes improved estimates for the neutron compound formation process. The purpose of this note is: (1) to compare the estimated crossmore » sections to current data files in both ENDF and ENDL databases; (2) to estimate ratios of cross sections relatively to {sup 235}U integrated over the ''tamped flattop'' critical assembly spectrum that was used in the earlier {sup 237}U report; and (3) to show the effect on the integral cross sections when the neutron capturing state is an excited rotational state or an isomer. The isomer and excited state results are shown for {sup 235}U and {sup 237}U.« less

Quality Management and Building Government Information Services.

ERIC Educational Resources Information Center

Farrell, Maggie

1998-01-01

Discusses serving library-patron needs in terms of customer service and quality control. Highlights include tools for measuring the quality of service (e.g., the SERVQUAL survey), advisory boards or focus groups, library "service statements," changing patron needs, new information formats, and justifying depository library services. (JAK)

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Principal component analysis as a tool for library design: a case study investigating natural products, brand-name drugs, natural product-like libraries, and drug-like libraries.

PubMed

Wenderski, Todd A; Stratton, Christopher F; Bauer, Renato A; Kopp, Felix; Tan, Derek S

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design.

Principal Component Analysis as a Tool for Library Design: A Case Study Investigating Natural Products, Brand-Name Drugs, Natural Product-Like Libraries, and Drug-Like Libraries

PubMed Central

Wenderski, Todd A.; Stratton, Christopher F.; Bauer, Renato A.; Kopp, Felix; Tan, Derek S.

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design. PMID:25618349

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

Clinedinst, Winston C.; Slominski, Christopher J.; Dickson, Richard W.; Wolverton, David A.

1993-01-01

The individual software processes used in the flight computers on-board the Advanced Transport Operating System (ATOPS) aircraft have many common functional elements. A library of commonly used software modules was created for general uses among the processes. The library includes modules for mathematical computations, data formatting, system database interfacing, and condition handling. The modules available in the library and their associated calling requirements are described.

Computer-Based Training for Library Staff: From Demonstration to Continuing Program.

ERIC Educational Resources Information Center

Bayne, Pauline S.

1993-01-01

Describes a demonstration project developed at the University of Tennessee (Knoxville) libraries to train nonprofessional library staff with computer-based training using HyperCard that was created by librarians rather than by computer programmers. Evaluation methods are discussed, including formative and summative evaluation; and modifications…

Plug into PR. NJLA Public Relations Handbook.

ERIC Educational Resources Information Center

New Jersey Library Association, Trenton.

A guide to using public relations techniques to promote both everyday services and special events at libraries, this handbook describes and suggests ways to use library displays; in-house printing; the local media, e.g., radio spots and cable television; library programs; marketing and promotion; and fundraising, including the formation of a…

Library Statistical Data Base Formats and Definitions.

ERIC Educational Resources Information Center

Jones, Dennis; And Others

Represented are the detailed set of data structures relevant to the categorization of information, terminology, and definitions employed in the design of the library statistical data base. The data base, or management information system, provides administrators with a framework of information and standardized data for library management, planning,…

Polyelemental nanoparticle libraries.

PubMed

Chen, Peng-Cheng; Liu, Xiaolong; Hedrick, James L; Xie, Zhuang; Wang, Shunzhi; Lin, Qing-Yuan; Hersam, Mark C; Dravid, Vinayak P; Mirkin, Chad A

2016-06-24

Multimetallic nanoparticles are useful in many fields, yet there are no effective strategies for synthesizing libraries of such structures, in which architectures can be explored in a systematic and site-specific manner. The absence of these capabilities precludes the possibility of comprehensively exploring such systems. We present systematic studies of individual polyelemental particle systems, in which composition and size can be independently controlled and structure formation (alloy versus phase-separated state) can be understood. We made libraries consisting of every combination of five metallic elements (Au, Ag, Co, Cu, and Ni) through polymer nanoreactor-mediated synthesis. Important insight into the factors that lead to alloy formation and phase segregation at the nanoscale were obtained, and routes to libraries of nanostructures that cannot be made by conventional methods were developed. Copyright © 2016, American Association for the Advancement of Science.

A highly functional synthetic phage display library containing over 40 billion human antibody clones.

PubMed

Weber, Marcel; Bujak, Emil; Putelli, Alessia; Villa, Alessandra; Matasci, Mattia; Gualandi, Laura; Hemmerle, Teresa; Wulhfard, Sarah; Neri, Dario

2014-01-01

Several synthetic antibody phage display libraries have been created and used for the isolation of human monoclonal antibodies. The performance of antibody libraries, which is usually measured in terms of their ability to yield high-affinity binding specificities against target proteins of interest, depends both on technical aspects (such as library size and quality of cloning) and on design features (which influence the percentage of functional clones in the library and their ability to be used for practical applications). Here, we describe the design, construction and characterization of a combinatorial phage display library, comprising over 40 billion human antibody clones in single-chain fragment variable (scFv) format. The library was designed with the aim to obtain highly stable antibody clones, which can be affinity-purified on protein A supports, even when used in scFv format. The library was found to be highly functional, as >90% of randomly selected clones expressed the corresponding antibody. When selected against more than 15 antigens from various sources, the library always yielded specific and potent binders, at a higher frequency compared to previous antibody libraries. To demonstrate library performance in practical biomedical research projects, we isolated the human antibody G5, which reacts both against human and murine forms of the alternatively spliced BCD segment of tenascin-C, an extracellular matrix component frequently over-expressed in cancer and in chronic inflammation. The new library represents a useful source of binding specificities, both for academic research and for the development of antibody-based therapeutics.

A Highly Functional Synthetic Phage Display Library Containing over 40 Billion Human Antibody Clones

PubMed Central

Weber, Marcel; Bujak, Emil; Putelli, Alessia; Villa, Alessandra; Matasci, Mattia; Gualandi, Laura; Hemmerle, Teresa; Wulhfard, Sarah; Neri, Dario

2014-01-01

Several synthetic antibody phage display libraries have been created and used for the isolation of human monoclonal antibodies. The performance of antibody libraries, which is usually measured in terms of their ability to yield high-affinity binding specificities against target proteins of interest, depends both on technical aspects (such as library size and quality of cloning) and on design features (which influence the percentage of functional clones in the library and their ability to be used for practical applications). Here, we describe the design, construction and characterization of a combinatorial phage display library, comprising over 40 billion human antibody clones in single-chain fragment variable (scFv) format. The library was designed with the aim to obtain highly stable antibody clones, which can be affinity-purified on protein A supports, even when used in scFv format. The library was found to be highly functional, as >90% of randomly selected clones expressed the corresponding antibody. When selected against more than 15 antigens from various sources, the library always yielded specific and potent binders, at a higher frequency compared to previous antibody libraries. To demonstrate library performance in practical biomedical research projects, we isolated the human antibody G5, which reacts both against human and murine forms of the alternatively spliced BCD segment of tenascin-C, an extracellular matrix component frequently over-expressed in cancer and in chronic inflammation. The new library represents a useful source of binding specificities, both for academic research and for the development of antibody-based therapeutics. PMID:24950200

Wettable and Unsinkable: The Hydrodynamics of Saccate Pollen Grains in Relation to the Pollination Mechanism in the Two New Zealand Species of Prumnopitys Phil. (Podocarpaceae)

PubMed Central

SALTER, JOSHUA; MURRAY, BRIAN G.; BRAGGINS, JOHN E.

2002-01-01

The pollination mechanism of most genera of the Podocarpaceae involves inverted ovules, a pollination drop and bisaccate pollen grains. Saccate grains have sometimes been referred to as ‘non‐wettable’ due to their buoyant properties, while non‐saccate pollen grains have been described as ‘wettable’. The hydrodynamic properties of saccate pollen grains of seven podocarp species in five genera, Dacrydium Sol. ex G. Forst., Dacrycarpus (Endl.) de Laub., Manoao Molloy, Podocarpus L‘Hér. ex Pers. and Prumnopitys Phil. have been tested in water, together with saccate and non‐saccate pollen of four other conifer genera, Cedrus Trew (Pinaceae), Cephalotaxus Siebold & Zucc. ex Endl. (Cephalotaxaceae), Cupressus L. (Cupressaceae) and Phyllocladus Rich. ex Mirb. (Phyllocladaceae), and spores of three fern species and one lycopod species. All four spore types studied were non‐wettable, whereas the bisaccate and trisaccate pollen types, like all other conifer pollen types, were wettable, enabling the grains to cross the surface tension barrier of water. Once past this barrier, grain behaviour was governed by presence or absence of sacci. Non‐saccate and vestigially saccate grains sank, whereas saccate grains behaved like air bubbles, floating up to the highest point. In addition, the grains were observed to float in water with sacci uppermost, consistent with the suggestion that distally placed sacci serve to orientate the germinal furrow of the pollen grain towards the nucellus of an inverted ovule. Observations of pollen grains in the pollen chambers of naturally pollinated Prumnopitys ovules confirmed this. The combination of buoyancy and wettability in saccate pollen has implications for the efficiency of the typical podocarp pollination mechanism. PMID:12099344

Clinical and academic use of electronic and print books: the Health Sciences Library System e-book study at the University of Pittsburgh

PubMed Central

Wessel, Charles B; Czechowski, Leslie J

2011-01-01

Objectives: The purpose of the Health Sciences Library System (HSLS) electronic book (e-book) study was to assess use, and factors affecting use, of e-books by all patron groups of an academic health sciences library serving both university and health system–affiliated patrons. Methods: A web-based survey was distributed to a random sample (n = 5,292) of holders of library remote access passwords. A total of 871 completed and 108 partially completed surveys were received, for an approximate response rate of 16.5%–18.5%, with all user groups represented. Descriptive and chi-square analysis was done using SPSS 17. Results: Library e-books were used by 55.4% of respondents. Use by role varied: 21.3% of faculty reported having assigned all or part of an e-book for class readings, while 86% of interns, residents, and fellows reported using an e-book to support clinical care. Respondents preferred print for textbooks and manuals and electronic format for research protocols, pharmaceutical, and reference books, but indicated high flexibility about format choice. They rated printing and saving e-book content as more important than annotation, highlighting, and bookmarking features. Conclusions: Respondents' willingness to use alternate formats, if convenient, suggests that libraries can selectively reduce title duplication between print and e-books and still support library user information needs, especially if publishers provide features that users want. Marketing and user education may increase use of e-book collections. PMID:21753914

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

Digital Preservation in Open-Source Digital Library Software

ERIC Educational Resources Information Center

Madalli, Devika P.; Barve, Sunita; Amin, Saiful

2012-01-01

Digital archives and digital library projects are being initiated all over the world for materials of different formats and domains. To organize, store, and retrieve digital content, many libraries as well as archiving centers are using either proprietary or open-source software. While it is accepted that print media can survive for centuries with…

Personnel for Research Libraries; Qualifications, Responsibilities and Use. Final Report.

ERIC Educational Resources Information Center

Clark, Philip M.

The project was conceived to examine the current manpower situation in research libraries and to develop a methodological model for projecting future personnel needs. Eight academic research libraries were selected for investigation and three instruments developed to gather data toward these ends. A personal interview format was used to interview…

Microform Catalogs: A Viable Alternative for Texas Libraries.

ERIC Educational Resources Information Center

Cox, Carolyn, M.; Juergens, Bonnie

This project proposed to develop and test the use of microform catalogs produced from computer-generated magnetic tape records in both fiche and film formats. The Computer Output Microform (COM) catalog developed for this purpose is a union list of titles from the five participating libraries--Houston and Dallas Public Libraries, Texas State…

Just Another Format: Integrating Resources for Users of Personal Digital Assistants

ERIC Educational Resources Information Center

Koufogiannakis, Denise; Ryan, Pam; Dahl, Susan

2005-01-01

This article discusses the integration of library resources for users of personal digital assistants (PDAs), with a focus on collections issues within an academic environment. The University of Alberta Libraries' PDA services initiative is used as an example of integrating services and resources into a library collection. Licensing issues, loaning…

Unwrapping the Bundle: An Examination of Research Libraries and the "Big Deal"

ERIC Educational Resources Information Center

Strieb, Karla L.; Blixrud, Julia C.

2014-01-01

This study presents and analyzes the findings of a 2012 survey of member libraries belonging to the Association of Research Libraries (ARL) about publishers' large journal bundles and compares the results to earlier surveys. The data illuminate five research questions: market penetration, journal bundle construction, collection format shifts,…

Using a Decision Grid Process to Build Consensus in Electronic Resources Cancellation Decisions

ERIC Educational Resources Information Center

Foudy, Gerri; McManus, Alesia

2005-01-01

Many libraries are expending an increasing part of their collections budgets on electronic resources. At the same time many libraries, especially those which are state funded, face diminishing budgets and high rates of inflation for serials subscriptions in all formats, including electronic resources. Therefore, many libraries need to develop ways…

Sesame IO Library User Manual Version 8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abhold, Hilary; Young, Ginger Ann

This document is a user manual for SES_IO, a low-level library for reading and writing sesame files. The purpose of the SES_IO library is to provide a simple user interface for accessing and creating sesame files that does not change across sesame format type (such as binary, ascii, and xml).

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

Redesigning a library-based genetics class research project through instructional theory and authentic experience*

PubMed Central

Tennant, Michele R; Edwards, Mary; Miyamoto, Michael M

2012-01-01

Question: How can the library-based research project of a genetics course be reinvigorated and made sustainable without sacrificing educational integrity? Setting: The University of Florida's Health Science Center Library provides the case study. Methods: Since 1996, the librarian has codeveloped, supported, and graded all components of the project. In 2009, the project evolved from a single-authored paper to a group-work poster, with graded presentations hosted by the library. In 2010, students were surveyed regarding class enhancements. Results: Responses indicated a preference for collaborative work and the poster format and suggested the changes facilitated learning. Instructors reported that the poster format more clearly documented students' understanding of genetics. Conclusion: Results suggest project enhancements contributed to greater appreciation, understanding, and application of classroom material and offered a unique and authentic learning experience, without compromising educational integrity. The library benefitted through increased visibility as a partner in the educational mission and development of a sustainable instructional collaboration. PMID:22514504

PNA-encoded chemical libraries.

PubMed

Zambaldo, Claudio; Barluenga, Sofia; Winssinger, Nicolas

2015-06-01

Peptide nucleic acid (PNA)-encoded chemical libraries along with DNA-encoded libraries have provided a powerful new paradigm for library synthesis and ligand discovery. PNA-encoding stands out for its compatibility with standard solid phase synthesis and the technology has been used to prepare libraries of peptides, heterocycles and glycoconjugates. Different screening formats have now been reported including selection-based and microarray-based methods that have yielded specific ligands against diverse target classes including membrane receptors, lectins and challenging targets such as Hsp70. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Library Research Course for Graduate and Professional Students in Communication Sciences and Disorders

ERIC Educational Resources Information Center

Tag, Sylvia G.

2007-01-01

This article describes the formation and content of a required library and information research course for graduate and professional students enrolled in the Communication Sciences and Disorders Master of Arts degree program at Western Washington University. The course was created as a result of library assessment, student feedback, and faculty…

Great Service Pays: A Model for Service Delivery in an Academic Music Library

ERIC Educational Resources Information Center

Wilson, Andrew M.

2007-01-01

Special-subject libraries can be particularly intimidating for casual and seasoned patrons alike. Music libraries, with their variety of materials, formats, and vocabularies, can present particular challenges for the user. With this proposal for a model of service delivery, as well as many tips gained through experience working the front-of-house…

78 FR 13645 - Notice of Public Meetings for the Draft Environmental Impact Statement and Draft Clean Air Act...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-28

... Conformity Determination in an open house format. DoN representatives will be available at informational... Determination are available for public review at the following libraries: 1. City of El Centro Public Library, 1140 North Imperial Avenue, El Centro, California 92243. 2. City of Imperial Public Library, 200 West...

Film Format Pandemonium

ERIC Educational Resources Information Center

Malczewski, Benjamin

2010-01-01

Every day, Americans borrow 2.1 million DVDs from public libraries. Barely beating libraries out for the top spot is Netflix, at 2.2 million daily rentals. This is according to the OCLC 2010 survey "How Libraries Stack Up." (Redbox vending-machine rentals lag behind at 1.1 million, while DVD rental chain Blockbuster is no longer in the running,…

Automation at the Fairfax County Virginia Library System.

ERIC Educational Resources Information Center

Baker, Alfred W.; And Others

The Fairfax County Library converted from a card catalog to a book catalog format in 1963. The first book catalogs were produced by the Sequential Card (SC) process. The master cards were prepared by the library and sent to Science Press, where copy was prepared on IBM cards, coded for sequential filing, and photographed to prepare page plates,…

"Space Capers." Texas Reading Club 1982: A Librarian's Planning Handbook.

ERIC Educational Resources Information Center

Rudd, Peggy Jemelka

Originally designed as a summer program to be offered through the network of bookmobiles and rural public libraries in the state, the Texas Reading Club is now also promoted year round by school and institutional libraries to encourage young readers and to acquaint them with libraries and their services. A theme, formats and ideas, and basic…

Streaming the Archives: Repurposing Systems to Advance a Small Media Digitization and Dissemination Program

ERIC Educational Resources Information Center

Anderson, Talea

2015-01-01

In 2013-2014, Brooks Library at Central Washington University (CWU) launched library content in three systems: a digital asset-management system, an institutional repository (IR), and a web-based discovery layer. In early 2014, the archives at the library began to use these systems to disseminate media recently digitized from legacy formats. As…

The Library Manager's Deskbook: 102 Expert Solutions to 101 Common Dilemmas.

ERIC Educational Resources Information Center

Carson, Paula Phillips; And Others

This is a handbook of advice for handling the everyday problems encountered in all types and sizes of libraries. It is designed to assist managers before, during, and after crises develop. Organized in an question-and-answer format, it tackles many dilemmas that can occur in the library, then offers solutions drawn from actual experience. The…

Networking among Gerontological and Geriatric Resource Centers: Summary of a Survey.

ERIC Educational Resources Information Center

Rafferty, Eve

The desirability and format of a network among libraries and resource centers serving the gerontological/geriatric field were addressed in a research project funded by the Special Libraries Association. Heads of 50 gerontological and 50 geriatric libraries were surveyed by mail to determine if there was interest in a joint network, i.e., a formal…

Traveling Uncharted Waters: The Exchange of Government Information between the United States and China.

ERIC Educational Resources Information Center

Wang, Rui

1998-01-01

Describes a program established between the United States and China for exchange of government publications through their national libraries, the Library of Congress and the National Library of China. Challenges to the program, including the shift to electronic formats in the United States and government Internet censorship in China, are…

Common Pitfalls in F77 Code Conversion

DTIC Science & Technology

2003-02-01

implementation versus another are the source of these errors rather than typography . It is well to use the practice of commenting-out original source file lines...identifier), every I in the format field must be replaced with f followed by an appropriate floating point format designator . Floating point numeric...helps even more. Finally, libraries are a major source of non-portablility[sic], with graphics libraries one of the chief culprits. We in Fusion

The virtual library: Coming of age

NASA Technical Reports Server (NTRS)

Hunter, Judy F.; Cotter, Gladys A.

1994-01-01

With the high speed networking capabilities, multiple media options, and massive amounts of information that exist in electronic format today, the concept of a 'virtual' library or 'library without walls' is becoming viable. In virtual library environment, the information processed goes beyond the traditional definition of documents to include the results of scientific and technical research and development (reports, software, data) recorded in any format or media: electronic, audio, video, or scanned images. Network access to information must include tools to help locate information sources and navigate the networks to connect to the sources, as well as methods to extract the relevant information. Graphical User Interfaces (GUI's) that are intuitive and navigational tools such as Intelligent Gateway Processors (IGP) will provide users with seamless and transparent use of high speed networks to access, organize, and manage information. Traditional libraries will become points of electronic access to information on multiple medias. The emphasis will be towards unique collections of information at each library rather than entire collections at every library. It is no longer a question of whether there is enough information available; it is more a question of how to manage the vast volumes of information. The future equation will involve being able to organize knowledge, manage information, and provide access at the point of origin.

Digital Libraries and the Problem of Purpose [and] On DigiPaper and the Dissemination of Electronic Documents [and] DFAS: The Distributed Finding Aid Search System [and] Best Practices for Digital Archiving: An Information Life Cycle Approach [and] Mapping and Converting Essential Federal Geographic Data Committee (FGDC) Metadata into MARC21 and Dublin Core: Towards an Alternative to the FGDC Clearinghouse [and] Evaluating Website Modifications at the National Library of Medicine through Search Log analysis.

ERIC Educational Resources Information Center

Levy, David M.; Huttenlocher, Dan; Moll, Angela; Smith, MacKenzie; Hodge, Gail M.; Chandler, Adam; Foley, Dan; Hafez, Alaaeldin M.; Redalen, Aaron; Miller, Naomi

2000-01-01

Includes six articles focusing on the purpose of digital public libraries; encoding electronic documents through compression techniques; a distributed finding aid server; digital archiving practices in the framework of information life cycle management; converting metadata into MARC format and Dublin Core formats; and evaluating Web sites through…

A comparison of the currency of secondary information sources in the biochemical literature. II. MEDLINE online and on CD-ROM.

PubMed

Grainger, F; Lyon, E

1992-12-01

The currency of selected versions of the MEDLINE database on CD-ROM and in online format was studied. The arrival of issues from 72 monthly journals and nine weekly titles during a 3-month period was monitored and their appearance in the various MEDLINE formats were recorded. Availability data for MEDLINE published by the National Library of Medicine were used as a baseline and subsequent distribution delays for the different MEDLINE formats were calculated. The study suggests a delay of approximately 2 weeks for indexing and mounting the MEDLINE file on to host computers for online access. A delay of 6-8 weeks was calculated for the MEDLINE data to be encoded on to compact disk, shipped and posted to the library customer. The currency of the MEDLINE database formats was compared with a weekly current-awareness service, CURRENT CONTENTS ON DISKETTE LIFE SCIENCES (CCOD). The majority of papers were indexed and distributed in CCOD within 10 weeks of publication date. Most papers appeared within 15 weeks in the online MEDLINE format and within 20 weeks in CD-ROM MEDLINE. The primary journal arrived at the library site within 5 weeks in most cases.

Comparison of the efficiency of antibody selection from semi-synthetic scFv and non-immune Fab phage display libraries against protein targets for rapid development of diagnostic immunoassays.

PubMed

Chan, Conrad E Z; Chan, Annie H Y; Lim, Angeline P C; Hanson, Brendon J

2011-10-28

Rapid development of diagnostic immunoassays against novel emerging or genetically modified pathogens in an emergency situation is dependent on the timely isolation of specific antibodies. Non-immune antibody phage display libraries are an efficient in vitro method for selecting monoclonal antibodies and hence ideal in these circumstances. Such libraries can be constructed from a variety of sources e.g. B cell cDNA or synthetically generated, and use a variety of antibody formats, typically scFv or Fab. However, antibody source and format can impact on the quality of antibodies generated and hence the effectiveness of this methodology for the timely production of antibodies. We have carried out a comparative screening of two antibody libraries, a semi-synthetic scFv library and a human-derived Fab library against the protective antigen toxin component of Bacillus anthracis and the epsilon toxin of Clostridium botulinum. We have shown that while the synthetic library produced a diverse collection of specific scFv-phage, these contained a high frequency of unnatural amber stops and glycosylation sites which limited their conversion to IgG, and also a high number which lost specificity when expressed as IgG. In contrast, these limitations were overcome by the use of a natural human library. Antibodies from both libraries could be used to develop sandwich ELISA assays with similar sensitivity. However, the ease and speed with which full-length IgG could be generated from the human-derived Fab library makes screening this type of library the preferable method for rapid antibody generation for diagnostic assay development. Copyright © 2011 Elsevier B.V. All rights reserved.

The 450th Jubilee of the Bavarian State Library: A Note

ERIC Educational Resources Information Center

Cope, R. L.

2008-01-01

To mark its founding in 1558 by Albrecht V., Duke of Bavaria, the Bavarian State Library (BSB) has issued a splendid catalogue (358 pages) with many sumptuous full-page coloured plates, taken from 113 works which were in the Library during its formative period 1558-1599). These works include manuscripts, church and secular music and early printed…

Beyond Failure: Potentially Mitigating Failed Author Searches in the Online Library Catalog through the Use of Linked Data

ERIC Educational Resources Information Center

Moulaison, Heather Lea; Stanley, Susan Nicole

2013-01-01

Linked data stores house vetted content that can supplement the information available through online library catalogs, potentially mitigating failed author searches if information about the author exists in linked data formats. In this case study, a total of 689 failed author index queries from a large Midwestern academic library's online library…

A Century of Change: The Evolution of School Library Resources, 1915-2015

ERIC Educational Resources Information Center

Lamb, Annette

2015-01-01

School libraries have been in existence since at least the eighth century. However, it wasn't until the twentieth century that the school library was seen primarily as "a source of enrichment for the curriculum, and a means of developing reading and study habits in the pupils" (Clyde 1981, 263). While the formats available and tools for…

Cutting Edge Books: The Impact of Digital Books on Public Library Acquisitions

ERIC Educational Resources Information Center

Taylor, Lisa

2008-01-01

The book has made the transition to the digital age; that much is certain. However, the jury is still out on what form or forms the book of the future will take and how libraries will adapt. This article is a look at the impact of digital books on public library acquisitions, including available formats, purchasing considerations, functional…

The German University of Library and Documentation Science.

ERIC Educational Resources Information Center

Kaegbein, P.

1982-01-01

Describes the formation of the University of Library and Documentation Sciences in Cologne and outlines the composition of the university's executive bodies, courses of studies offered, and academic degrees granted to certified librarians and documentalists. (EJS)

Monte Carlo Determination of Gamma Ray Exposure from a Homogeneous Ground Plane

DTIC Science & Technology

1990-03-01

A HOMOGENEOUS GROUND PLANE SOURCE THESIS Presented to the Faculty of the School of Engineering of the Air Force Institute of Technology Air University...come from a standard ANISN format library called FEWG1-85. This state-of-the- art cross section library which contains 37 neutron energy groups and 21...purpose. The FEWGl library, a state-of-the- art cross section library developed for the Defense Nuclear Agency con- sisting of 21 gamma-ray enerQj

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

Release of the ENDF/B-VII.1 Evaluated Nuclear Data File

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, David

2012-06-30

The Cross Section Evaluation Working Group (CSEWG) released the ENDF/B-VII.1 library on December 22, 2011. The ENDF/B-VII.1 library is CSEWG's latest recommended evaluated nuclear data file for use in nuclear science and technology applications, and incorporates advances made in the five years since the release of ENDF/B-VII.0, including: many new evaluation in the neutron sublibrary (423 in all and over 190 of these contain covariances), new fission product yields and a greatly improved decay data sublibrary. This summary barely touches on the five years worth of advances present in the ENDF/B-VII.1 library. We expect that these changes will lead tomore » improved integral performance in reactors and other applications. Furthermore, the expansion of covariance data in this release will allow for better uncertainty quantification, reducing design margins and costs. The ENDF library is an ongoing and evolving effort. Currently, the ENDF data community embarking on several parallel efforts to improve library management: (1) The adoption of a continuous integration system to provide evaluators 'instant' feedback on the quality of their evaluations and to provide data users with working 'beta' quality libraries in between major releases. (2) The transition to new hierarchical data format - the Generalized Nuclear Data (GND) format. We expect GND to enable new kinds of evaluated data which cannot be accommodated in the legacy ENDF format. (3) The development of data assimilation and uncertainty propagation techniques to enable the consistent use of integral experimental data in the evaluation process.« less

Archimedes' principle for characterisation of recombinant whole cell biocatalysts.

PubMed

Schmitt, Steven; Walser, Marcel; Rehmann, Michael; Oesterle, Sabine; Panke, Sven; Held, Martin

2018-02-14

The ability of whole cells to catalyse multistep reactions, often yielding synthetically demanding compounds later used by industrial biotech or pharma, makes them an indispensable tool of synthetic chemistry. The complex reaction network employed by cellular catalysts and the still only moderate predictive power of modelling approaches leaves this tool challenging to engineer. Frequently, large libraries of semi-rationally generated variants are sampled in high-throughput mode in order to then identify improved catalysts. We present a method for space- and time-efficient processing of very large libraries (10 7 ) of recombinant cellular catalysts, in which the phenotypic characterisation and the isolation of positive variants for the entire library is done within one minute in a single, highly parallelized operation. Specifically, product formation in nanolitre-sized cultivation vessels is sensed and translated into the formation of catalase as a reporter protein. Exposure to hydrogen peroxide leads to oxygen gas formation and thus to a density shift of the cultivation vessel. Exploiting Archimedes' principle, this density shift and the resulting upward buoyancy force can be used for batch-wise library sampling. We demonstrate the potential of the method for both, screening and selection protocols, and envision a wide applicability of the system for biosensor-based assays.

Transport of calcium ions through a bulk membrane by use of a dynamic combinatorial library.

PubMed

Saggiomo, Vittorio; Lüning, Ulrich

2009-07-07

In a bulk membrane transport experiment, a dynamic combinatorial library (DCL) has been used to transport calcium ions; the calcium ions amplify the formation of a macrocyclic carrier which results in transport.

Glutathione and abscisic acid supplementation influences somatic embryo maturation and hormone endogenous levels during somatic embryogenesis in Podocarpus lambertii Klotzsch ex Endl.

PubMed

Fraga, Hugo Pacheco de Freitas; Vieira, Leila do Nascimento; Puttkammer, Catarina Corrêa; Dos Santos, Henrique Pessoa; Garighan, Julio de Andrade; Guerra, Miguel Pedro

2016-12-01

Here we propose a protocol for embryogenic cultures induction, proliferation and maturation for the Brazilian conifer Podocarpus lambertii, and investigated the effect of abscisic acid (ABA) and glutathione (GSH) supplementation on the maturation phase. ABA, zeatin (Z) and salicylic acid (SA) endogenous levels were quantified. Number of somatic embryos obtained in ABA-supplemented treatment was significant higher than in ABA-free treatment, showing the relevance of ABA supplementation during somatic embryos maturation. Histological analysis showed the stereotyped sequence of developmental stages in conifer somatic embryos, reaching the late torpedo-staged embryo. GSH supplementation in maturation culture medium improved the somatic embryos number and morphological features. GSH 0mM and GSH 0.1mM treatments correlated with a decreased ABA endogenous level during maturation, while GSH 0.5mM treatment showed constant levels. All treatments resulted in decreased Z endogenous levels, supporting the concept that cytokinins are important during the initial cell division but not for the later stages of embryo development. The lowest SA levels found in GSH 0.5mM treatment were coincident with early embryonic development, and this treatment resulted in the highest development of somatic embryos. Thus, a correlation between lower SA levels and improved somatic embryo formation can be hypothesized. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

ProMC: Input-output data format for HEP applications using varint encoding

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; May, E.; Strand, K.; Van Gemmeren, P.

2014-10-01

A new data format for Monte Carlo (MC) events, or any structural data, including experimental data, is discussed. The format is designed to store data in a compact binary form using variable-size integer encoding as implemented in the Google's Protocol Buffers package. This approach is implemented in the PROMC library which produces smaller file sizes for MC records compared to the existing input-output libraries used in high-energy physics (HEP). Other important features of the proposed format are a separation of abstract data layouts from concrete programming implementations, self-description and random access. Data stored in PROMC files can be written, read and manipulated in a number of programming languages, such C++, JAVA, FORTRAN and PYTHON.

USGS Spectral Library Version 7

USGS Publications Warehouse

Kokaly, Raymond F.; Clark, Roger N.; Swayze, Gregg A.; Livo, K. Eric; Hoefen, Todd M.; Pearson, Neil C.; Wise, Richard A.; Benzel, William M.; Lowers, Heather A.; Driscoll, Rhonda L.; Klein, Anna J.

2017-04-10

We have assembled a library of spectra measured with laboratory, field, and airborne spectrometers. The instruments used cover wavelengths from the ultraviolet to the far infrared (0.2 to 200 microns [μm]). Laboratory samples of specific minerals, plants, chemical compounds, and manmade materials were measured. In many cases, samples were purified, so that unique spectral features of a material can be related to its chemical structure. These spectro-chemical links are important for interpreting remotely sensed data collected in the field or from an aircraft or spacecraft. This library also contains physically constructed as well as mathematically computed mixtures. Four different spectrometer types were used to measure spectra in the library: (1) Beckman™ 5270 covering the spectral range 0.2 to 3 µm, (2) standard, high resolution (hi-res), and high-resolution Next Generation (hi-resNG) models of Analytical Spectral Devices (ASD) field portable spectrometers covering the range from 0.35 to 2.5 µm, (3) Nicolet™ Fourier Transform Infra-Red (FTIR) interferometer spectrometers covering the range from about 1.12 to 216 µm, and (4) the NASA Airborne Visible/Infra-Red Imaging Spectrometer AVIRIS, covering the range 0.37 to 2.5 µm. Measurements of rocks, soils, and natural mixtures of minerals were made in laboratory and field settings. Spectra of plant components and vegetation plots, comprising many plant types and species with varying backgrounds, are also in this library. Measurements by airborne spectrometers are included for forested vegetation plots, in which the trees are too tall for measurement by a field spectrometer. This report describes the instruments used, the organization of materials into chapters, metadata descriptions of spectra and samples, and possible artifacts in the spectral measurements. To facilitate greater application of the spectra, the library has also been convolved to selected spectrometer and imaging spectrometers sampling and bandpasses, and resampled to selected broadband multispectral sensors. The native file format of the library is the SPECtrum Processing Routines (SPECPR) data format. This report describes how to access freely available software to read the SPECPR format. To facilitate broader access to the library, we produced generic formats of the spectra and metadata in text files. The library is provided on digital media and online at https://speclab.cr.usgs.gov/spectral-lib.html. A long-term archive of these data are stored on the USGS ScienceBase data server (https://dx.doi.org/10.5066/F7RR1WDJ).

By-product formation in repetitive PCR amplification of DNA libraries during SELEX.

PubMed

Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

2014-01-01

The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.

Transportation library connectivity pooled fund study, TPF-5(105).

DOT National Transportation Integrated Search

2010-10-01

This report is a record of the formation, major activities and accomplishments of the Transportation Library Connectivity : pooled fund study, TPF-5(105), from its approval by FHWA in 2005 through its fifth and final annual meeting in September : 201...

Agroecosystems & Environment | National Agricultural Library

Science.gov Websites

Skip to main content Home National Agricultural Library United States Department of Agriculture Ag useful formats (maps, tables, graphs), Agricultural Products html Useful to Usable: Developing usable integrated expertise in applied climatology, crop modeling, agronomy, cyber-technology, agricultural

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

PubMed Central

Hubert, Casey R J; Oldenburg, Thomas B P; Fustic, Milovan; Gray, Neil D; Larter, Stephen R; Penn, Kevin; Rowan, Arlene K; Seshadri, Rekha; Sherry, Angela; Swainsbury, Richard; Voordouw, Gerrit; Voordouw, Johanna K; Head, Ian M

2012-01-01

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems. PMID:21824242

Developing an academic medical library core journal collection in the (almost) post-print era: the Florida State University College of Medicine Medical Library experience

PubMed Central

Shearer, Barbara S.; Nagy, Suzanne P.

2003-01-01

The Florida State University (FSU) College of Medicine Medical Library is the first academic medical library to be established since the Web's dramatic appearance during the 1990s. A large customer base for electronic medical information resources is both comfortable with and eager to migrate to the electronic format completely, and vendors are designing radical pricing models that make print journal cancellations economically advantageous. In this (almost) post-print environment, the new FSU Medical Library is being created and will continue to evolve. By analyzing print journal subscription lists of eighteen academic medical libraries with similar missions to the community-based FSU College of Medicine and by entering these and selected quality indicators into a Microsoft Access database, a core list was created. This list serves as a selection guide, as a point for discussion with faculty and curriculum leaders when creating budgets, and for financial negotiations in a broader university environment. After journal titles specific to allied health sciences, veterinary medicine, dentistry, pharmacy, library science, and nursing were eliminated from the list, 4,225 unique journal titles emerged. Based on a ten-point scale including SERHOLD holdings and DOCLINE borrowing activity, a list of 449 core titles is identified. The core list has been saved in spreadsheet format for easy sorting by a number of parameters. PMID:12883565

Developing an academic medical library core journal collection in the (almost) post-print era: the Florida State University College of Medicine Medical Library experience.

PubMed

Shearer, Barbara S; Nagy, Suzanne P

2003-07-01

The Florida State University (FSU) College of Medicine Medical Library is the first academic medical library to be established since the Web's dramatic appearance during the 1990s. A large customer base for electronic medical information resources is both comfortable with and eager to migrate to the electronic format completely, and vendors are designing radical pricing models that make print journal cancellations economically advantageous. In this (almost) post-print environment, the new FSU Medical Library is being created and will continue to evolve. By analyzing print journal subscription lists of eighteen academic medical libraries with similar missions to the community-based FSU College of Medicine and by entering these and selected quality indicators into a Microsoft Access database, a core list was created. This list serves as a selection guide, as a point for discussion with faculty and curriculum leaders when creating budgets, and for financial negotiations in a broader university environment. After journal titles specific to allied health sciences, veterinary medicine, dentistry, pharmacy, library science, and nursing were eliminated from the list, 4,225 unique journal titles emerged. Based on a ten-point scale including SERHOLD holdings and DOCLINE borrowing activity, a list of 449 core titles is identified. The core list has been saved in spreadsheet format for easy sorting by a number of parameters.

Java Image I/O for VICAR, PDS, and ISIS

NASA Technical Reports Server (NTRS)

Deen, Robert G.; Levoe, Steven R.

2011-01-01

This library, written in Java, supports input and output of images and metadata (labels) in the VICAR, PDS image, and ISIS-2 and ISIS-3 file formats. Three levels of access exist. The first level comprises the low-level, direct access to the file. This allows an application to read and write specific image tiles, lines, or pixels and to manipulate the label data directly. This layer is analogous to the C-language "VICAR Run-Time Library" (RTL), which is the image I/O library for the (C/C++/Fortran) VICAR image processing system from JPL MIPL (Multimission Image Processing Lab). This low-level library can also be used to read and write labeled, uncompressed images stored in formats similar to VICAR, such as ISIS-2 and -3, and a subset of PDS (image format). The second level of access involves two codecs based on Java Advanced Imaging (JAI) to provide access to VICAR and PDS images in a file-format-independent manner. JAI is supplied by Sun Microsystems as an extension to desktop Java, and has a number of codecs for formats such as GIF, TIFF, JPEG, etc. Although Sun has deprecated the codec mechanism (replaced by IIO), it is still used in many places. The VICAR and PDS codecs allow any program written using the JAI codec spec to use VICAR or PDS images automatically, with no specific knowledge of the VICAR or PDS formats. Support for metadata (labels) is included, but is format-dependent. The PDS codec, when processing PDS images with an embedded VIAR label ("dual-labeled images," such as used for MER), presents the VICAR label in a new way that is compatible with the VICAR codec. The third level of access involves VICAR, PDS, and ISIS Image I/O plugins. The Java core includes an "Image I/O" (IIO) package that is similar in concept to the JAI codec, but is newer and more capable. Applications written to the IIO specification can use any image format for which a plug-in exists, with no specific knowledge of the format itself.

Connecting with health science students and faculty to facilitate the design of a mobile library website.

PubMed

Grabowsky, Adelia; Wright, Melissa

2013-01-01

Observing increasing usage of smartphones by students and faculty of the University of Mississippi Medical Center, librarians at Rowland Medical Library decided to explore student and faculty interest in a mobile website for the library. Focus groups were held to examine interest in a site, essential resources to include on a site, and format of the site itself. The study found significant interest in the development of a mobile library website; additionally, participants believed it essential that the site be simple and easy to use and that only certain library resources should be included on the site.

Target-induced formation of neuraminidase inhibitors from in vitro virtual combinatorial libraries

PubMed Central

Hochgürtel, Matthias; Kroth, Heiko; Piecha, Dorothea; Hofmann, Michael W.; Nicolau, Claude; Krause, Sonja; Schaaf, Otmar; Sonnenmoser, Gabriele; Eliseev, Alexey V.

2002-01-01

Neuraminidase, a key enzyme responsible for influenza virus propagation, has been used as a template for selective synthesis of small subsets of its own inhibitors from theoretically highly diverse dynamic combinatorial libraries. We show that the library building blocks, aldehydes and amines, form significant amounts of the library components resulting from their coupling by reductive amination only in the presence of the enzyme. The target amplifies the best hits at least 120-fold. The dynamic libraries synthesized and screened in such an in vitro virtual mode form the components that possess high inhibitory activity, as confirmed by enzyme assays with independently synthesized individual compounds. PMID:11891312

Using Newsletters in the Library's Communication Strategy.

ERIC Educational Resources Information Center

Bryce, Betty K.

1996-01-01

Examines the practical aspects of publishing a newsletter as a communication tool for libraries. Both internal and external newsletters are discussed, along with ones concerned with fundraising or ones in electronic format. Other topics include editorship, staffing, content decisions, production techniques, distribution, and organizational…

Denver Public Library Western History/Genealogy Digital Collections

Science.gov Websites

Denver Public Library's Western History/Genealogy Department collection of digitized photographs Mountain Division Records" "Photographs - Western History" To limit your search by format @denverlibrary.org or 720-865-1818. More Resources: Genealogy Railroad Photographs Denver History, Buildings

Library of Michigan: Financial Management Reference Guide.

ERIC Educational Resources Information Center

Michigan Library, Lansing.

Developed to provide library directors, staff, and board members with information for performing accounting and financial management functions, this guide answers frequently asked questions, describes common practices and processes, provides examples and suggested formats for selected financial reports, and identifies issues that may require…

37 CFR 202.3 - Registration of copyright.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... 202.3 Section 202.3 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS... digital format (if eligible) along with the application and payment, or a remitter may send physical... Information Office, Library of Congress. Printed form applications may be completed and submitted by...

EDI at the Jet Propulsion Laboratory Library

NASA Technical Reports Server (NTRS)

Amago, B.

1994-01-01

The JPL Library and Information Center orders and claims material elecronically whenever feasible. The NASA Aerospace Research Information Network (ARIN) is used to order books for the library collection; BIP Plus on CD-ROM is used to order office copies. Paper copies of invoices are processed when material is received. Subscriptions are ordered using the vendor's online system; monthly and annual invoices are received both in paper and electronic format (diskette of FTP). Library-developed dbase programs complement or duplicate functions available through ARIN and/or the JPL institutional accounting system.

Academic Libraries: Myths and Realities. Proceedings of the National Conference of the Association of College and Research Libraries (3rd, Seattle, Washington, April 4-7, 1984).

ERIC Educational Resources Information Center

Dodson, Suzanne C., Ed.; Menges, Gary L., Ed.

The 56 papers in this proceedings are divided into three groups--theme, alternative format, and contributed papers. Myths and realities are explored in the first group as they relate to university, college, community, and junior college libraries, and to private sector information utilities. The conference wrap-up session is included in this…

OCLC In Retrospect; A Review Of the Impact of the OCLC System On the Administration of a Large University Technical Services Operations.

ERIC Educational Resources Information Center

Nitecki, Joseph Z.

The paper expresses the viewpoint of the author, based on his own two-year experience in supervising the use of the on-line Ohio College Library Center (OCLC) system in Temple University Library. The report contains a brief description of the formation of the Philadelphia Area Library Network (PALINET) and it lists some problems dealt with by…

Year of the Oceans: Science of Information Handling. [Proceedings of the] Annual Conference of the International Association of Marine Science Libraries and Information Centers (10th, Woods Hole, Massachusetts, October 2-5, 1984).

ERIC Educational Resources Information Center

Grundy, R. L., Ed.; Ford, R. T., Ed.

International Association of Marine Science Libraries and Information Centers (IAMSLIC) conferences provide a format for libraries and information specialists to discuss common interests and concerns so that services and information can be made available to scientists, administrators, engineers, educators and students in the discipline of marine…

The U.S. Federal Depository Library Program and U.S. Government Information in an Electronic Environment: Issues for the Transition and the Millennium.

ERIC Educational Resources Information Center

Powell, Margaret S.

Since 1895, the Federal Depository Library Program (FDLP), administered by the U.S. Government Printing Office (GPO), has provided no-fee public access to information generated by the U.S. government through a network of libraries. For 200 years, print-on-paper remained the dominant format. By 1978, publications were also distributed in…

E-library Implementation in Library University of Riau

NASA Astrophysics Data System (ADS)

Yuhelmi; Rismayeti

2017-12-01

This research aims to see how the e-book implementation in Library University of Riau and the obstacle in its implementation. In the Globalization era, digital libraries should be developed or else it will decrease the readers’ interest, with the recent advanced technology, digital libraries are one of the learning tools that can be used to finding an information through the internet access, hence digital libraries or commonly known as E-Library is really helping the students and academic community in finding information. The methods that used in this research is Observation, Interview, and Literature Study. The respondents in this research are the staff who involved in the process of digitization in Library University of Riau. The result of this research shows that implementation of e-library in Library University of Riau is already filled the user needs for now, although there is obstacle faced just like technical problems for example the internet connection speed and the technical problem to convert the format from Microsoft Word .doc to Adobe.pdf

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

PubMed

Smelter, Andrey; Moseley, Hunter N B

2018-01-01

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package. This Python package, named 'mwtab', is a parser for the domain-specific 'mwTab' flat file format, which provides facilities for reading, accessing, and writing 'mwTab' formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given 'mwTab' formatted file. In order to develop the 'mwtab' package we used the official 'mwTab' format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. The 'mwtab' package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating 'mwTab' formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, 'pythonic' access and manipulation of data and metadata. Also, the package provides facilities to convert 'mwTab' files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The 'mwtab' package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between 'mwTab' and JSONized formats in raw text and a variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

A transposon mutant library of Bacillus cereus ATCC 10987 reveals novel genes required for biofilm formation and implicates motility as an important factor for pellicle-biofilm formation.

PubMed

Okshevsky, Mira; Louw, Matilde Greve; Lamela, Elena Otero; Nilsson, Martin; Tolker-Nielsen, Tim; Meyer, Rikke Louise

2018-04-01

Bacillus cereus is one of the most common opportunistic pathogens causing foodborne illness, as well as a common source of contamination in the dairy industry. B. cereus can form robust biofilms on food processing surfaces, resulting in food contamination due to shedding of cells and spores. Despite the medical and industrial relevance of this species, the genetic basis of biofilm formation in B. cereus is not well studied. In order to identify genes required for biofilm formation in this bacterium, we created a library of 5000 +  transposon mutants of the biofilm-forming strain B. cereusATCC 10987, using an unbiased mariner transposon approach. The mutant library was screened for the ability to form a pellicle biofilm at the air-media interface, as well as a submerged biofilm at the solid-media interface. A total of 91 genes were identified as essential for biofilm formation. These genes encode functions such as chemotaxis, amino acid metabolism and cellular repair mechanisms, and include numerous genes not previously known to be required for biofilm formation. Although the majority of disrupted genes are not directly responsible for motility, further investigations revealed that the vast majority of the biofilm-deficient mutants were also motility impaired. This observation implicates motility as a pivotal factor in the formation of a biofilm by B. cereus. These results expand our knowledge of the fundamental molecular mechanisms of biofilm formation by B. cereus. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

What's Cooking in the School Library Media Center?

ERIC Educational Resources Information Center

Barron, Daniel D.

2001-01-01

Discusses ways in which cooking and food can be used to integrate school library media programs into the curriculum. Topics include gender consciousness; family literacy; alternative formats for special physical or learning challenges; history and social studies applications; world cultures; and cookbooks and literature. (LRW)

Video Recordings in Public Libraries.

ERIC Educational Resources Information Center

Doyle, Stephen

1984-01-01

Reports on development and operation of public library collection of video recordings, describes results of user survey conducted over 6-month period, and offers brief guidelines. Potential users, censorship and copyright, organization of collection, fees, damage and loss, funding, purchasing and promotion, formats, processing and cataloging,…

Library Information Resource Book For Staff.

ERIC Educational Resources Information Center

Potts, Ken; And Others

This guide is the Northern Illinois University (NIU) Libraries' quick reference tool for providing information about its collections, facilities, and services. The articles are arranged in an alphabetic, dictionary format with numerous cross-references, and highlight information on the following: administrative offices; company annual reports;…

37 CFR 202.3 - Registration of copyright.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... 202.3 Section 202.3 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS.... Deposit materials in support of the online application may be submitted electronically in a digital format... request to the Copyright Public Information Office, Library of Congress. Printed form applications may be...

Virtually Usable: A Test of the Information Gardens

ERIC Educational Resources Information Center

Johnson, Megan; Ochoa, Louise; Purpur, Geraldine

2007-01-01

This paper presents the results of a usability study conducted to determine the functionality of a desktop, three-dimensional virtual library designed and supported by the Appalachian State University Distance Learning Library Services team. Formative evaluations were performed with representative students utilizing Morae software. Results…

HDF-EOS 2 and HDF-EOS 5 Compatibility Library

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

The HDF-EOS 2 and HDF-EOS 5 Compatibility Library contains C-language functions that provide uniform access to HDF-EOS 2 and HDF-EOS 5 files through one set of application programming interface (API) calls. ("HDFEOS 2" and "HDF-EOS 5" are defined in the immediately preceding article.) Without this library, differences between the APIs of HDF-EOS 2 and HDF-EOS 5 would necessitate writing of different programs to cover HDF-EOS 2 and HDF-EOS 5. The API associated with this library is denoted "he25." For nearly every HDF-EOS 5 API call, there is a corresponding he25 API call. If a file in question is in the HDF-EOS 5 format, the code reverts to the corresponding HDF-EOS 5 call; if the file is in the HDF-EOS 2 format, the code translates the arguments to HDF-EOS 2 equivalents (if necessary), calls the HDFEOS 2 call, and retranslates the results back to HDF-EOS 5 (if necessary).

MODIS Technical Report Series. Volume 4: MODIS data access user's guide: Scan cube format

NASA Technical Reports Server (NTRS)

Kalb, Virginia L.; Goff, Thomas E.

1994-01-01

The software described in this document provides I/O functions to be used with Moderate Resolution Spectroradiometer (MODIS) level 1 and 2 data, and could be easily extended to other data sources. This data is in a scan cube data format: a 3-dimensional ragged array containing multiple bands which have resolutions ranging from 250 to 1000 meters. The complexity of the data structure is handled internally by the library. The I/O calls allow the user to access any pixel in any band through 'C' structure syntax. The high MODIS data volume (approaching half a terabyte per day) has been a driving factor in the library design. To avoid recopying data for user access, all I/O is performed through dynamic 'C' pointer manipulation. This manual contains background material on MODIS, several coding examples of library usage, in-depth discussions of each function, reference 'man' type pages, and several appendices with details of the included files used to customize a user's data product for use with the library.

By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX

PubMed Central

Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

2014-01-01

The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection. PMID:25490402

Convergence Toward Common Standards in Machine-Readable Cataloging *

PubMed Central

Gull, C. D.

1969-01-01

The adoption of the MARC II format for the communication of bibliographic information by the three National Libraries of the U.S.A. makes it possible for those libraries to converge on the remaining necessary common standards for machine-readable cataloging. Three levels of standards are identified: fundamental, the character set; intermediate, MARC II; and detailed, the codes for identifying data elements. The convergence on these standards implies that the National Libraries can create and operate a Joint Bibliographic Data Bank requiring standard book numbers and universal serial numbers for identifying monographs and serials and that the system will thoroughly process contributed catalog entries before adding them to the Data Bank. There is reason to hope that the use of the MARC II format will facilitate catalogers' decision processes. PMID:5782261

Development of Communities of Practice in School Library Education

ERIC Educational Resources Information Center

Burns, Elizabeth A.; Howard, Jody K.; Kimmel, Sue C.

2016-01-01

To properly prepare pre-service school librarians, school library educators in online courses must provide opportunities for collaborative engagement. This collaborative education should also recognize the pedagogical benefit of the organic formation of communities of practice that develop within areas outside of curriculum content. This…

Libraries, Self-Censorship, and Information Technologies.

ERIC Educational Resources Information Center

Buschman, John

1994-01-01

Explores the theme of self-censorship in libraries in relation to new technologies. Highlights include the results of investing in high-cost electronic resources at the expense of traditional, lower-status formats; the effect of information technologies on literacy and historical records; and market censorship, including centralization and…

The Future Role of Librarians in the Virtual Library Environment.

ERIC Educational Resources Information Center

Burke, Liz

2002-01-01

Considers the role of librarians in a virtual library environment. Highlights include providing intellectual access to information in any format; evaluating available sources of information; organizing information; ensuring the preservation of information; providing specialized staff to help meet information needs; and the economic impact of…

Promoting Learning in Libraries through Information Literacy.

ERIC Educational Resources Information Center

Breivik, Patricia Senn; Ford, Barbara J.

1993-01-01

Discusses information literacy and describes activities under the sponsorship of the National Forum on Information Literacy (NFIL) that promotes information literacy in schools and libraries. Activities of member organizations of the NFIL are described, including policy formation, publications, and programs; and the role of the American Library…

Processing and validation of JEFF-3.1.1 and ENDF/B-VII.0 group-wise cross section libraries for shielding calculations

NASA Astrophysics Data System (ADS)

Pescarini, M.; Sinitsa, V.; Orsi, R.; Frisoni, M.

2013-03-01

This paper presents a synthesis of the ENEA-Bologna Nuclear Data Group programme dedicated to generate and validate group-wise cross section libraries for shielding and radiation damage deterministic calculations in nuclear fission reactors, following the data processing methodology recommended in the ANSI/ANS-6.1.2-1999 (R2009) American Standard. The VITJEFF311.BOLIB and VITENDF70.BOLIB finegroup coupled n-γ (199 n + 42 γ - VITAMIN-B6 structure) multi-purpose cross section libraries, based on the Bondarenko method for neutron resonance self-shielding and respectively on JEFF-3.1.1 and ENDF/B-VII.0 evaluated nuclear data, were produced in AMPX format using the NJOY-99.259 and the ENEA-Bologna 2007 Revision of the SCAMPI nuclear data processing systems. Two derived broad-group coupled n-γ (47 n + 20 γ - BUGLE-96 structure) working cross section libraries in FIDO-ANISN format for LWR shielding and pressure vessel dosimetry calculations, named BUGJEFF311.BOLIB and BUGENDF70.BOLIB, were generated by the revised version of SCAMPI, through problem-dependent cross section collapsing and self-shielding from the cited fine-group libraries. The validation results on the criticality safety benchmark experiments for the fine-group libraries and the preliminary validation results for the broad-group working libraries on the PCA-Replica and VENUS-3 engineering neutron shielding benchmark experiments are reported in synthesis.

DSPSR: Digital Signal Processing Software for Pulsar Astronomy

NASA Astrophysics Data System (ADS)

van Straten, W.; Bailes, M.

2010-10-01

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

The mathematics of a successful deconvolution: a quantitative assessment of mixture-based combinatorial libraries screened against two formylpeptide receptors.

PubMed

Santos, Radleigh G; Appel, Jon R; Giulianotti, Marc A; Edwards, Bruce S; Sklar, Larry A; Houghten, Richard A; Pinilla, Clemencia

2013-05-30

In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays.

LiveInventor: An Interactive Development Environment for Robot Autonomy

NASA Technical Reports Server (NTRS)

Neveu, Charles; Shirley, Mark

2003-01-01

LiveInventor is an interactive development environment for robot autonomy developed at NASA Ames Research Center. It extends the industry-standard OpenInventor graphics library and scenegraph file format to include kinetic and kinematic information, a physics-simulation library, an embedded Scheme interpreter, and a distributed communication system.

Promoting U.S. Census Data in an Academic Environment: Opportunities and Challenges.

ERIC Educational Resources Information Center

Ragains, Patrick

1995-01-01

Discusses efforts at the Montana State University (Bozeman) library to promote use of census data. Describes instructional sessions, and budgetary and service issues faced by depository libraries providing access to census data in electronic formats. Also includes copies of handouts from the instructional sessions. (Author/AEF)

BOXER: Fine-flux Cross Section Condensation, 2D Few Group Diffusion and Transport Burnup Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

2010-02-01

Neutron transport, calculation of multiplication factor and neutron fluxes in 2-D configurations: cell calculations, 2-D diffusion and transport, and burnup. Preparation of a cross section library for the code BOXER from a basic library in ENDF/B format (ETOBOX).

Common Bibliographic Standards for Baylor University Libraries. Revised.

ERIC Educational Resources Information Center

Scott, Sharon; And Others

Developed by a Baylor University (Texas) Task Force, the revised policies of bibliographic standards for the university libraries provide formats for: (1) archives and manuscript control; (2) audiovisual media; (3) books; (4) machine-readable data files; (5) maps; (6) music scores; (7) serials; and (8) sound recordings. The task force assumptions…

CD-ROM and Libraries.

ERIC Educational Resources Information Center

Murphy, Brower

1985-01-01

The Compact Disc-Read Only Memory (CD-ROM) data format is explained and illustrated, noting current and potential applications. The "5-inch" compact laserdisc is described and photographs of an IBM PC/Hitachi CD-ROM system adopted by Library Corporation to support its MARC database--BiblioFile--are presented. Screen displays for…

Compressed Continuous Computation v. 12/20/2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorodetsky, Alex

2017-02-17

A library for performing numerical computation with low-rank functions. The (C3) library enables performing continuous linear and multilinear algebra with multidimensional functions. Common tasks include taking "matrix" decompositions of vector- or matrix-valued functions, approximating multidimensional functions in low-rank format, adding or multiplying functions together, integrating multidimensional functions.

Library Dream Machines: Helping Students Master Super Online Catalogs.

ERIC Educational Resources Information Center

Webb, T. D.

1992-01-01

Describes how automation has transformed the library and how super-catalogs have affected the process of doing research. Explains how faculty and librarians can work together to help students to use the available databases effectively, by teaching them Boolean logic, standard record formats, filing rules, etc. (DMM)

MARC: Mrs. Avram's Remarkable Contribution.

ERIC Educational Resources Information Center

Rather, Lucia J.; Wiggins, Beacher

1989-01-01

This discussion of the contributions of Henriette D. Avram to the field of librarianship covers her role in establishing MARC formats as the international standard for library automation and her work in the retrospective conversion of catalogs, establishment of library standards, and creation of information networks. An interview with Dr. Avram is…

lawn: An R client for the Turf JavaScript Library for Geospatial Analysis

EPA Science Inventory

lawn is an R package to provide access to the geospatial analysis capabilities in the Turf javascript library. Turf expects data in GeoJSON format. Given that many datasets are now available natively in GeoJSON providing an easier method for conducting geospatial analyses on thes...

Software for Processing Flight and Simulated Data of the ATIC Experiment

NASA Technical Reports Server (NTRS)

Panov, A. D.; Adams, J. H., Jr.; Ahn, H. S.; Bashindzhagyan, G. L.; Batkov, K. E.; Case, G.; Christl, M.; Chang, J.; Fazely, A. R.; Ganel, O.;

State of the art of geoscience libraries and information services

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruett, N.J.

Geoscience libraries and geoscience information services are closely related. Both are trying to meet the needs of the geoscientists for information and data. Both are also being affected by many trends: increased availability of personal computers; decreased costs of machine readable storage; increased availability of maps in digital format (Pallatto, 1986); progress in graphic displays and in developing Geographic Information System, (GIS) (Kelly and Phillips, 1986); development in artificial intelligence; and the availability of new formats (e.g. CD-ROM). Some additional factors are at work at changing the role of libraries: libraries are coming to recognize the impossibility of collecting everythingmore » and the validity of Bradford's Law unobtrustive studies of library reference services have pointed out that only 50% of the questions are answered correctly it is clear that the number of databases is increasing although good figures for specifically geoscience databases are not available; lists of numeric database are beginning to appear; evaluative (as opposed to purely descriptive) reviews of available bibliographic databases are beginning to appear; more and more libraries are getting online catalogs and results of studies of users of online catalog are being used to improve catalog design; and research is raising consciousness about the value of; and research is raising consciousness about the value of information. All these trends are having or will have an effect on geoscience information.« less

SU-E-J-93: Development of Pre-Contoured Human Model Library in DICOM-RT Format for the Epidemiological Study of the Radiotherapy Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyakuryal, A; Lee, C; Lee, C

Purpose: Prior to 3D conformal radiation therapy planning, patient anatomy information was mostly limited to 2D beams-eye-view from the conventional simulator. To analyze the outcomes of such treatments for radiation late effects, 3D computational human models are often used in commercial treatment planning systems (TPSs). However, several underlying difficulties such as time-consuming manual delineation procedures of a large number of structures in the model have always limited its applications. Primary objective of this work was to develop a human model library for the epidemiological study by converting 3D-surface model organs to DICOM-RT format (DICOM-RT structure) using an in-house built software.more » We converted the ICRP reference human models to DICOM-RT models, which can be readily adopted for various dose calculations. Methods: MATLAB based code were utilized to convert the contour drawings extracted in text-format from the 3D graphic-tool, Rhinoceros into DICOM-RT structure format for 50 different organs of each model using a 16GB dual-core processor. The conversion periods were measured for each DICOM-RT models, and the reconstructed structure volumes were validated against the original 3D-surface models in the TPS. Ten reference hybrid whole-body models (8-pediatric and 2-adults) were automatically processed to create DICOM-RT computational human model library. Results: Mean contour conversion period was found to be 580 (N=2) and 394.5 (N=8) seconds for 50 organs in the adult and pediatric models respectively. A good agreement for large organs (NRMSD <1.0%) and small organs (NRMSD <7.7%) was also observed between the original volumes and corresponding DICOM-RT structure volumes of the organs. Conclusion: The ICRP reference human models were converted into DICOM-RT format to support the epidemiological study using a large cohort of conventional radiotherapy patients. Due to its DICOM-compatibility, the library may be implemented to many other different applications. We also expect to develop the library by including additional models in future.« less

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

NASA Astrophysics Data System (ADS)

García, Alberto; Verstraete, Matthieu J.; Pouillon, Yann; Junquera, Javier

2018-06-01

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability.

Scaling up the 454 Titanium Library Construction and Pooling of Barcoded Libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phung, Wilson; Hack, Christopher; Shapiro, Harris

2009-03-23

We have been developing a high throughput 454 library construction process at the Joint Genome Institute to meet the needs of de novo sequencing a large number of microbial and eukaryote genomes, EST, and metagenome projects. We have been focusing efforts in three areas: (1) modifying the current process to allow the construction of 454 standard libraries on a 96-well format; (2) developing a robotic platform to perform the 454 library construction; and (3) designing molecular barcodes to allow pooling and sorting of many different samples. In the development of a high throughput process to scale up the number ofmore » libraries by adapting the process to a 96-well plate format, the key process change involves the replacement of gel electrophoresis for size selection with Solid Phase Reversible Immobilization (SPRI) beads. Although the standard deviation of the insert sizes increases, the overall quality sequence and distribution of the reads in the genome has not changed. The manual process of constructing 454 shotgun libraries on 96-well plates is a time-consuming, labor-intensive, and ergonomically hazardous process; we have been experimenting to program a BioMek robot to perform the library construction. This will not only enable library construction to be completed in a single day, but will also minimize any ergonomic risk. In addition, we have implemented a set of molecular barcodes (AKA Multiple Identifiers or MID) and a pooling process that allows us to sequence many targets simultaneously. Here we will present the testing of pooling a set of selected fosmids derived from the endomycorrhizal fungus Glomus intraradices. By combining the robotic library construction process and the use of molecular barcodes, it is now possible to sequence hundreds of fosmids that represent a minimal tiling path of this genome. Here we present the progress and the challenges of developing these scaled-up processes.« less

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

PubMed

Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

2018-01-02

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Long-term data archiving

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, David Steven

2009-01-01

Long term data archiving has much value for chemists, not only to retain access to research and product development records, but also to enable new developments and new discoveries. There are some recent regulatory requirements (e.g., FDA 21 CFR Part 11), but good science and good business both benefit regardless. A particular example of the benefits of and need for long term data archiving is the management of data from spectroscopic laboratory instruments. The sheer amount of spectroscopic data is increasing at a scary rate, and the pressures to archive come from the expense to create the data (or recreatemore » it if it is lost) as well as its high information content. The goal of long-term data archiving is to save and organize instrument data files as well as any needed meta data (such as sample ID, LIMS information, operator, date, time, instrument conditions, sample type, excitation details, environmental parameters, etc.). This editorial explores the issues involved in long-term data archiving using the example of Raman spectral databases. There are at present several such databases, including common data format libraries and proprietary libraries. However, such databases and libraries should ultimately satisfy stringent criteria for long term data archiving, including readability for long times into the future, robustness to changes in computer hardware and operating systems, and use of public domain data formats. The latter criterion implies the data format should be platform independent and the tools to create the data format should be easily and publicly obtainable or developable. Several examples of attempts at spectral libraries exist, such as the ASTM ANDI format, and the JCAMP-DX format. On the other hand, proprietary library spectra can be exchanged and manipulated using proprietary tools. As the above examples have deficiencies according to the three long term data archiving criteria, Extensible Markup Language (XML; a product of the World Wide Web Consortium, an independent standards body) as a new data interchange tool is being investigated and implemented. In order to facilitate data archiving, Raman data needs calibration as well as some other kinds of data treatment. Figure 1 illustrates schematically the present situation for Raman data calibration in the world-wide Raman spectroscopy community, and presents some of the terminology used.« less

Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists.

PubMed

Miersch, Shane; Maruthachalam, Bharathikumar Vellalore; Geyer, C Ronald; Sidhu, Sachdev S

2017-05-19

We tested whether grafting an interaction domain into the hypervariable loop of a combinatorial antibody library could promote targeting to a specific epitope. Formation of the epidermal growth factor receptor (EGFR) signaling heterodimer involves extensive contacts mediated by a "dimerization loop." We grafted the dimerization loop into the third hypervariable loop of a synthetic antigen-binding fragment (Fab) library and diversified other loops using a tailored diversity strategy. This structure-directed Fab library and a naı̈ve synthetic Fab library were used to select Fabs against EGFR. Both libraries yielded high affinity Fabs that bound to overlapping epitopes on cell-surface EGFR, inhibited receptor activation, and targeted epitopes distinct from those of cetuximab and panitumumab. Epitope mapping experiments revealed complex sites of interaction, comprised of domains I and II but not exclusively localized to the receptor dimerization loop. These results validate the grafting approach for designing Fab libraries and also underscore the versatility of naı̈ve synthetic libraries.

The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors

PubMed Central

Santos, Radleigh G.; Appel, Jon R.; Giulianotti, Marc A.; Edwards, Bruce S.; Sklar, Larry A.; Houghten, Richard A.; Pinilla, Clemencia

2014-01-01

In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays. PMID:23722730

An open library of CT patient projection data

NASA Astrophysics Data System (ADS)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Holmes, David; Fletcher, Joel; McCollough, Cynthia

2016-03-01

Lack of access to projection data from patient CT scans is a major limitation for development and validation of new reconstruction algorithms. To meet this critical need, we are building a library of CT patient projection data in an open and vendor-neutral format, DICOM-CT-PD, which is an extended DICOM format that contains sinogram data, acquisition geometry, patient information, and pathology identification. The library consists of scans of various types, including head scans, chest scans, abdomen scans, electrocardiogram (ECG)-gated scans, and dual-energy scans. For each scan, three types of data are provided, including DICOM-CT-PD projection data at various dose levels, reconstructed CT images, and a free-form text file. Several instructional documents are provided to help the users extract information from DICOM-CT-PD files, including a dictionary file for the DICOM-CT-PD format, a DICOM-CT-PD reader, and a user manual. Radiologist detection performance based on the reconstructed CT images is also provided. So far 328 head cases, 228 chest cases, and 228 abdomen cases have been collected for potential inclusion. The final library will include a selection of 50 head, chest, and abdomen scans each from at least two different manufacturers, and a few ECG-gated scans and dual-source, dual-energy scans. It will be freely available to academic researchers, and is expected to greatly facilitate the development and validation of CT reconstruction algorithms.

Strike Up the Score: Deriving Searchable and Playable Digital Formats from Sheet Music; Smart Objects and Open Archives; Building the Archives of the Future: Advanced in Preserving Electronic Records at the National Archives and Records Administration; From the Digitized to the Digital Library.

ERIC Educational Resources Information Center

Choudhury, G. Sayeed; DiLauro, Tim; Droettboom, Michael; Fujinaga, Ichiro; MacMillan, Karl; Nelson, Michael L.; Maly, Kurt; Thibodeau, Kenneth; Thaller, Manfred

2001-01-01

These articles describe the experiences of the Johns Hopkins University library in digitizing their collection of sheet music; motivation for buckets, Smart Object, Dumb Archive (SODA) and the Open Archives Initiative (OAI), and initial experiences using them in digital library (DL) testbeds; requirements for archival institutions, the National…

Systems Design and Pilot Operation of a Regional Center for Technical Processing for the Libraries of the New England State Universities. NELINET, New England Library Information Network. Progress Report, July 1, 1967 - March 30, 1968, Volume II, Appendices.

ERIC Educational Resources Information Center

Agenbroad, James E.; And Others

Included in this volume of appendices to LI 000 979 are acquisitions flow charts; a current operations questionnaire; an algorithm for splitting the Library of Congress call number; analysis of the Machine-Readable Cataloging (MARC II) format; production problems and decisions; operating procedures for information transmittal in the New England…

The Contingent Valuation Method in Public Libraries

ERIC Educational Resources Information Center

Chung, Hye-Kyung

2008-01-01

This study aims to present a new model measuring the economic value of public libraries, combining the dissonance minimizing (DM) and information bias minimizing (IBM) format in the contingent valuation (CV) surveys. The possible biases which are tied to the conventional CV surveys are reviewed. An empirical study is presented to compare the model…

Instructing the Academic Library User: Historical Background and Utilization of Audiovisual Presentations.

ERIC Educational Resources Information Center

Whitmore, Marilyn P.

A brief sketch of the trends in bibliographic instruction from the 30's through the 70's introduces this review of the literature on applications of instructional media in programs for academic library users. Formats discussed include television, programmed instruction, multimedia presentations, and slide/tape presentations. The slide/tape program…

Design of Formats and Packs of Catalog Cards.

ERIC Educational Resources Information Center

OCLC Online Computer Library Center, Inc., Dublin, OH.

The three major functions of the Ohio College Library Center's Shared Cataloging System are: 1) provision of union catalog location listing; 2) making available cataloging done by one library to all other users of the system; and 3) production of catalog cards. The system, based on a central machine readable data base, speeds cataloging and…

Automated Acquisition, Cataloging, and Circulation in a Large Research Library.

ERIC Educational Resources Information Center

Boylan, Merle N.; And Others

This report describes automated procedures now in use for book acquisition, and book and document cataloging and circulation, in the library at Lawrence Radiation Laboratory, Livermore. The purpose of the automation is to increase frequency and accuracy of record updatings, decrease the time required to maintain records, improve the formats of the…

The Heinz Electronic Library Interactive On-line System (HELIOS): An Update.

ERIC Educational Resources Information Center

Galloway, Edward A.; Michalek, Gabrielle V.

1998-01-01

Describes a project at Carnegie Mellon University libraries to convert the congressional papers of the late Senator John Heinz to digital format and to create an online system to search and retrieve these papers. Highlights include scanning, optical character recognition, and a search engine utilizing natural language processing. (Author/LRW)

The Publishing of Library and Information Science Journals in Southeast Asia--An Overview.

ERIC Educational Resources Information Center

Yeow-fei, Jaffe Yee

This paper presents an overview of the present state of the publishing activities of library and information science journals in Southeast Asia, focusing on format, circulation/readership, quality, and editorial focus. It also highlights some of the important titles from Thailand, Malaysia, Singapore, the Philippines, Indonesia, Brunei, Vietnam,…

FRBR Cataloging's Future Is Closer than You Think!

ERIC Educational Resources Information Center

Adamich, Tom

2007-01-01

Through the decades, the kinds of materials found in libraries have grown and changed, adapting to the needs of library users as well as economic, social, and even environmental factors. Similarly, the presentation format for cataloging content has changed. Another change is about to emerge in cataloging, and its name is FRBR (Functional…

Assessing Information on the Internet: Toward Providing Library Services for Computer-Mediated Communication. A Final Report.

ERIC Educational Resources Information Center

Dillon, Martin; And Others

The Online Computer Library Center Internet Resource project focused on the nature of electronic textual information available through remote access using the Internet and the problems associated with creating machine-readable cataloging (MARC) records for these objects using current USMARC format for computer files and "Anglo-American…

ALEPH: Israel's Research Library Network: Background, Evolution, and Implications for Networking in a Small Country.

ERIC Educational Resources Information Center

Lazinger, Susan S.

1991-01-01

Describes ALEPH, the research library network in Israel, and analyzes the strengths and weaknesses of its decentralized structure. Highlights include comparisons between RLIN and ALEPH; centralized versus decentralized networks; the format of ALEPH; authority control in ALEPH; and non-Roman scripts in both networks. (16 references) (LRW)

Technical Processing Librarians in the 1980's: Current Trends and Future Forecasts.

ERIC Educational Resources Information Center

Kennedy, Gail

1980-01-01

This review of recent and anticipated advances in library automation technology and methodology includes a review of the effects of OCLC, MARC formatting, AACR2, and increasing costs, as well as predictions of the impact on library technical processing of networking, expansion of automation, minicomputers, specialized reference services, and…

Nurturing Your Media

ERIC Educational Resources Information Center

Donohue, Nanette

2008-01-01

No other category of library materials has grown more quickly in the last several decades than audiovisual (AV), nor has any other category undergone so many changes in format. The transitions from vinyl records to 8-tracks to audiocassettes to CDs and from film reel to 3/4" U-Matic to VHS to DVD have impacted library services tremendously. The…

Children of the Book: Parents, Bedtime, and Jewish Identity

ERIC Educational Resources Information Center

Alexander, Shelley T.

2013-01-01

This article offers a conceptual framework for assessing PJ Library programming grounded in the relevant scholarly literature and illustrated by way of conversations with PJ Library parents. It is built around three themes concerning how parents view their role as facilitators in their child's religious and cultural identity formation through the…

The Role of the Access Services Manager in the Virtual Library

ERIC Educational Resources Information Center

Jetton, Lora Lennertz; Bailey, Alberta S.

2010-01-01

This article updates a previous article published in 1992 that described the role of the access services manager in policy formation. Since that time, the access services department and mission has matured and evolved to a prominent position within the library organization. Technological changes and innovation in the marketplace of wired and…

Transition to Electronic Access of Government Information: Are the Depository Libraries Prepared?

ERIC Educational Resources Information Center

Vaughan, Liwen Qiu; Dolan, Elizabeth

1998-01-01

Examines the readiness of depository libraries in Canada to adopt new technologies for disseminating government publications. Findings are reported on current use of different publication formats, type of help sought by users, staff skills and training needs, adequacy of physical and financial resources, support from governing bodies, and…

Use of Information and Communication Technology to Enhance the Information Literacy Skills of Distance Students

ERIC Educational Resources Information Center

Pastula, Matthew

2010-01-01

Information and Communication Technology (ICT) has become an integral tool in enhancing library services worldwide. This article looks at ways technology is utilized at Massey University to bridge the gap between distance students and traditional library services. There are a variety of software providers, formats and implementation practices…

STILTS -- Starlink Tables Infrastructure Library Tool Set

NASA Astrophysics Data System (ADS)

Taylor, Mark

STILTS is a set of command-line tools for processing tabular data. It has been designed for, but is not restricted to, use on astronomical data such as source catalogues. It contains both generic (format-independent) table processing tools and tools for processing VOTable documents. Facilities offered include crossmatching, format conversion, format validation, column calculation and rearrangement, row selection, sorting, plotting, statistical calculations and metadata display. Calculations on cell data can be performed using a powerful and extensible expression language. The package is written in pure Java and based on STIL, the Starlink Tables Infrastructure Library. This gives it high portability, support for many data formats (including FITS, VOTable, text-based formats and SQL databases), extensibility and scalability. Where possible the tools are written to accept streamed data so the size of tables which can be processed is not limited by available memory. As well as the tutorial and reference information in this document, detailed on-line help is available from the tools themselves. STILTS is available under the GNU General Public Licence.

Application of new technologies in the virtual library: Seminars in Turkey, Portugal, and Spain

NASA Technical Reports Server (NTRS)

Hunter, Judy F.; Cotter, Gladys A.

1994-01-01

This paper focuses on the technologies that are available today to support the concept of a virtual library. The concept of a 'virtual library' or a 'library without walls' is meant to convey the idea that information in any format should be available to the end-user from the desktop as if it were located on the local workstation. Discussed here are the background, trends, technology enablers, end-user requirements, and the NASA Access Mechanism (NAM) system, one example of how it is possible to apply existing technologies to the client server architecture to logically centralize geographically distributed applications and information.

Damsel: A Data Model Storage Library for Exascale Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhary, Alok; Liao, Wei-keng

Computational science applications have been described as having one of seven motifs (the “seven dwarfs”), each having a particular pattern of computation and communication. From a storage and I/O perspective, these applications can also be grouped into a number of data model motifs describing the way data is organized and accessed during simulation, analysis, and visualization. Major storage data models developed in the 1990s, such as Network Common Data Format (netCDF) and Hierarchical Data Format (HDF) projects, created support for more complex data models. Development of both netCDF and HDF5 was influenced by multi-dimensional dataset storage requirements, but their accessmore » models and formats were designed with sequential storage in mind (e.g., a POSIX I/O model). Although these and other high-level I/O libraries have had a beneficial impact on large parallel applications, they do not always attain a high percentage of peak I/O performance due to fundamental design limitations, and they do not address the full range of current and future computational science data models. The goal of this project is to enable exascale computational science applications to interact conveniently and efficiently with storage through abstractions that match their data models. The project consists of three major activities: (1) identifying major data model motifs in computational science applications and developing representative benchmarks; (2) developing a data model storage library, called Damsel, that supports these motifs, provides efficient storage data layouts, incorporates optimizations to enable exascale operation, and is tolerant to failures; and (3) productizing Damsel and working with computational scientists to encourage adoption of this library by the scientific community. The product of this project, Damsel library, is openly available for download from http://cucis.ece.northwestern.edu/projects/DAMSEL. Several case studies and application programming interface reference are also available to assist new users to learn to use the library.« less

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation

PubMed Central

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-01-01

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events. PMID:15840720

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation.

PubMed

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-04-26

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events.

A UNIMARC Bibliographic Format Database for ABCD

ERIC Educational Resources Information Center

Megnigbeto, Eustache

2012-01-01

Purpose: ABCD is a web-based open and free software suite for library management derived from the UNESCO CDS/ISIS software technology. The first version was launched officially in December 2009 with a MARC 21 bibliographic format database. This paper aims to detail the building of the UNIMARC bibliographic format database for ABCD.…

Screening of Small Molecule Interactor Library by Using In-Cell NMR Spectroscopy (SMILI-NMR)

PubMed Central

Xie, Jingjing; Thapa, Rajiv; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander

2011-01-01

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP–FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast. PMID:19422228

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity.

PubMed

Chen, Hong-Ming; Armstrong, Zachary; Hallam, Steven J; Withers, Stephen G

2016-02-08

Screening of large enzyme libraries such as those derived from metagenomic sources requires sensitive substrates. Fluorogenic glycosides typically offer the best sensitivity but typically must be used in a stopped format to generate good signal. Use of fluorescent phenols of pKa < 7, such as halogenated coumarins, allows direct screening at neutral pH. The synthesis and characterisation of a set of nine different glycosides of 6-chloro-4-methylumbelliferone are described. The use of these substrates in a pooled format for screening of expressed metagenomic libraries yielded a "hit rate" of 1 in 60. Hits were then readily deconvoluted with the individual substrates in a single plate to identify specific activities within each clone. The use of such a collection of substrates greatly accelerates the screening process. Copyright © 2015 Elsevier Ltd. All rights reserved.

The EPRDATA Format: A Dialogue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, III, Henry Grady

2015-08-18

Recently the Los Alamos Nuclear Data Team has communicated certain issues of concern in relation to the new electron/photon/relaxation ACE data format as released in the eprdata12 library. In this document those issues are parsed, analyzed, and answered.

UNICON: A Powerful and Easy-to-Use Compound Library Converter.

PubMed

Sommer, Kai; Friedrich, Nils-Ole; Bietz, Stefan; Hilbig, Matthias; Inhester, Therese; Rarey, Matthias

2016-06-27

The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs. This paper describes UNICON, an easy-to-use software tool for this task. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles. For this purpose, UNICON bundles the key elements of the previously described NAOMI library in a single, easy-to-use command line tool.

SVGenes: a library for rendering genomic features in scalable vector graphic format.

PubMed

Etherington, Graham J; MacLean, Daniel

2013-08-01

Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements. SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion. The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License. dan.maclean@tsl.ac.uk.

Libraries for the Blind in the Information Age: Guidelines for Development. IFLA Professional Reports, No. 86

ERIC Educational Resources Information Center

Kavanagh, Rosemary, Ed.; Skold, Beatrice Christensen, Ed.

2005-01-01

Visually impaired people have the same information needs as sighted people. Just as sighted people might read a newspaper, listen to a CD or download electronic information from the Internet, visually impaired people also want access to relevant information in their chosen accessible format. Developing an efficient library service for…

Music for Blind and Physically Handicapped Individuals. Fact Sheet.

ERIC Educational Resources Information Center

Library of Congress, Washington, DC. National Library Service for the Blind and Physically Handicapped.

With the cooperation of composers and publishers who grant permission to use copyrighted works, the National Library Service for the Blind and Physically Handicapped (NLS) of the Library of Congress selects and produces music scores in braille and large-print formats, and music magazines and books about music and musicians in large-print, braille,…

Using Formative & Summative Assessment to Evaluate Library Instruction in an Online First Year Writing Course

ERIC Educational Resources Information Center

Haber, Natalie; Mitchell, Tiffany N.

2017-01-01

Ensuring quality library instruction in an online-exclusive First Year Writing (FYW) course is important and challenging. Assessing what the students learned and how is equally important. The authors collaborate and co-teach the information literacy portion of an online-exclusive second semester FYW course at the University of Tennessee at…

NOAA Photo Library

Science.gov Websites

reached the mature stage of formation. Image ID: nssl0065, NOAA's National Severe Storms Laboratory (NSSL Available Publication of the U.S. Department of Commerce, National Oceanic & Atmospheric Adminstration NOAA Photo Library Banner Takes you to the Top Page Takes you to the About this Site page. Takes

NOAA Photo Library

Science.gov Websites

in its early stage of formation. Image ID: nssl0061, NOAA's National Severe Storms Laboratory (NSSL Available Publication of the U.S. Department of Commerce, National Oceanic & Atmospheric Adminstration NOAA Photo Library Banner Takes you to the Top Page Takes you to the About this Site page. Takes

NOAA Photo Library

Science.gov Websites

in its early stage of formation. Image ID: nssl0062, NOAA's National Severe Storms Laboratory (NSSL Available Publication of the U.S. Department of Commerce, National Oceanic & Atmospheric Adminstration NOAA Photo Library Banner Takes you to the Top Page Takes you to the About this Site page. Takes

NOAA Photo Library

Science.gov Websites

in its early stage of formation. Image ID: nssl0064, NOAA's National Severe Storms Laboratory (NSSL Available Publication of the U.S. Department of Commerce, National Oceanic & Atmospheric Adminstration NOAA Photo Library Banner Takes you to the Top Page Takes you to the About this Site page. Takes

N-N bond formation in Ugi processes: from nitric acid to libraries of nitramines.

PubMed

Mercalli, Valentina; Nyadanu, Aude; Cordier, Marie; Tron, Gian Cesare; Grimaud, Laurence; El Kaim, Laurent

2017-02-09

The Ugi reaction has drawn considerable attention over the years leading to numerous libraries of heterocycles and various extensions changing the nature of the components of the coupling. We report here the use of nitric acid as carboxylic acids surrogates, displaying the first aminative Ugi-type reaction leading to nitramines.

Research Libraries in OCLC: A Quarterly, Numbers 1-4, January-October 1981.

ERIC Educational Resources Information Center

Research Libraries in OCLC: A Quarterly, 1981

1981-01-01

The articles in these four issues include discussions of: the Research Libraries Advisory Committee to OCLC; Title II-C grants for bibliographic access/control research projects; cooperative cataloging costs via OCLC; a research project on online public access; an OCLC examination of the UK-MARC format; use of the Comprehensive Index (CINDEX) and…

Rapid Prototyping a Collections-Based Mobile Wayfinding Application

ERIC Educational Resources Information Center

Hahn, Jim; Morales, Alaina

2011-01-01

This research presents the results of a project that investigated how students use a library developed mobile app to locate books in the library. The study employed a methodology of formative evaluation so that the development of the mobile app would be informed by user preferences for next generation wayfinding systems. A key finding is the…

Redesigning the OPAC: Moving outside the ILMS

ERIC Educational Resources Information Center

Sokvitne, Lloyd O.

2006-01-01

The need to develop new OPACs that meet the needs of users better is becoming well acknowledged. How libraries can transform their OPACs to modern web friendly formats is not yet clear. This paper describes the State Library of Tasmania's experience in developing a new OPAC by exporting bibliographic data to a software package outside the ILMS.…

Proposed Computer System for Library Catalog Maintenance. Part II: System Design.

ERIC Educational Resources Information Center

Stein (Theodore) Co., New York, NY.

The logic of the system presented in this report is divided into six parts for computer processing and manipulation. They are: (1) processing of Library of Congress copy, (2) editing of input into standard format, (3) processing of information into and out from the authority files, (4) creation of the catalog records, (5) production of the…

Research Maps New Routes for Reading Success in PLA Early Childhood Initiative.

ERIC Educational Resources Information Center

Meyers, Elaine

2002-01-01

The Public Library Association (PLA) partnered with the National Institute of Child Health and Human Development (NICHD) to develop research-based tools for parents to prepare children for reading. Inherent in the materials is the major role of the public library in formation of readers. Outlines goals and activities (2001-2002) of the PLA/ALSC…

The Art of Change: The Impact of Place and the Future of Academic Art Library Collections

ERIC Educational Resources Information Center

Falls, Sarah; Hatheway, Holly

2015-01-01

Academic institutions have long supported stand-alone branch libraries devoted to fine arts, architecture, and other allied fields. As subject specific collecting on campuses has been decentralized by collaborative collection development, consortial borrowing, and the quick availability of materials in both digital and print formats, the need for…

The Unlimited Potential of the Electronic Library (Except Where Prohibited by the Copyright Law).

ERIC Educational Resources Information Center

Schmidt, Steven; Lewis, David

This paper describes the creation of a new library facility for Indiana University-Purdue University at Indianapolis, one designed ready to accommodate an infrastructure that would support the new technologies of the electronic information environment. Wiring and fiber-optic schemes are outlined briefly. The document is formatted as a script for…

Academic Library Media Usage: Faculty and Student Use of the Independent Learning Center.

ERIC Educational Resources Information Center

Besemer, Susan P.

This report describes a spring 1982 survey of faculty and student users and nonusers of library audiovisual collections at the State University of New York (SUNY)-Buffalo. User frequency, the composition of user patronage, preferred media formats for learning, and users' perceptions of audiovisual services offered are described. A brief history is…

Quality in Context: A Guide to Certification and Registration by the Medical Library Association.

ERIC Educational Resources Information Center

Fitzsimons, Eileen; Mayfield, M. Kent

This guide is designed to assist prospective examinees in preparing for the certification/registration examination of the Medical Library Association (MLA). The format of the examination and the types of questions to be found on the examination are discussed, and suggestions for test preparation are provided. Several practice "mini"…

Scholarly Use of E-Books in a Virtual Academic Environment: A Case Study

ERIC Educational Resources Information Center

Ahmad, Pervaiz; Brogan, Mark

2012-01-01

From a fledgling technology with no proven business models, electronic books (e-books) have grown in importance usurping traditional formats as an acquisitions budget line in many academic library contexts. Business models include purchase, subscription, and pay per use. In academic and research libraries, web based e-book delivery is the dominant…

Web-based document image processing

NASA Astrophysics Data System (ADS)

Walker, Frank L.; Thoma, George R.

1999-12-01

Increasing numbers of research libraries are turning to the Internet for electron interlibrary loan and for document delivery to patrons. This has been made possible through the widespread adoption of software such as Ariel and DocView. Ariel, a product of the Research Libraries Group, converts paper-based documents to monochrome bitmapped images, and delivers them over the Internet. The National Library of Medicine's DocView is primarily designed for library patrons are beginning to reap the benefits of this new technology, barriers exist, e.g., differences in image file format, that lead to difficulties in the use of library document information. To research how to overcome such barriers, the Communications Engineering Branch of the Lister Hill National Center for Biomedical Communications, an R and D division of NLM, has developed a web site called the DocMorph Server. This is part of an ongoing intramural R and D program in document imaging that has spanned many aspects of electronic document conversion and preservation, Internet document transmission and document usage. The DocMorph Server Web site is designed to fill two roles. First, in a role that will benefit both libraries and their patrons, it allows Internet users to upload scanned image files for conversion to alternative formats, thereby enabling wider delivery and easier usage of library document information. Second, the DocMorph Server provides the design team an active test bed for evaluating the effectiveness and utility of new document image processing algorithms and functions, so that they may be evaluated for possible inclusion in other image processing software products being developed at NLM or elsewhere. This paper describes the design of the prototype DocMorph Server and the image processing functions being implemented on it.

SLHAplus: A library for implementing extensions of the standard model

NASA Astrophysics Data System (ADS)

Bélanger, G.; Christensen, Neil D.; Pukhov, A.; Semenov, A.

2011-03-01

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules. Program summaryProgram title: SLHAplus_1.3 Catalogue identifier: AEHX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 6283 No. of bytes in distributed program, including test data, etc.: 52 119 Distribution format: tar.gz Programming language: C Computer: IBM PC, MAC Operating system: UNIX (Linux, Darwin, Cygwin) RAM: 2000 MB Classification: 11.1 Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables. Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses. Running time: 0.001 sec

Interface Between CDS/ISIS and the Web at the Library of the Cagliari Observatory

NASA Astrophysics Data System (ADS)

Mureddu, Leonardo; Denotti, Franca; Alvito, Gianni

The library catalog of the Cagliari Observatory was digitized some years ago, by using CDS/ISIS with a practical format named ``ASTCA'' derived from the well-known ``BIBLO''. Recently the observatory has put some effort into the creation and maintenance of a Web site; on that occasion the library database has been interfaced to the Web server by means of the software WWWISIS and a locally created search form. Both books and journals can be searched by remote users. Book searches can be made by authors, titles or keywords.

Persistence of El Niño effects on stable isotope ratios in cellulose of Coast Redwood tree-rings

NASA Astrophysics Data System (ADS)

Johnstone, J. A.

2005-12-01

An anomalously wet El Niño winter in 1998 in Sonoma County, California, USA produced sharp changes in the oxygen and carbon isotope ratios of tree-ring cellulose of Coast Redwood ( Sequoia sempervirens (D.Don) Endl.) which persisted for several years thereafter. High-resolution cellulose sampling reveals a negative shift in both δ18O and δ13C, consistent with greater reliance on winter rain water supplies (rather than summer fog) as well as reduced drought stress due to the anomalous precipitation. The annual cycle of these isotopic ratios is also muted for several years following the 1998 winter. These observations suggest a disproportionate and persistent influence of extreme years in the interannual variability of Coast Redwood hydrology and physiology.

The Effect of a Poster, Display, and Recommended Listening List on the Circulation of Audiobooks in the Public Library.

ERIC Educational Resources Information Center

Kucalaba, Linda

Previous studies have found that the librarian's use of book displays and recommended lists are an effective means to increase circulation in the public library. Yet conflicting results were found when these merchandising techniques were used with collection materials in the nonprint format, specifically audiobooks and videos, instead of books.…

Digitization and the Creation of Virtual Libraries: The Princeton University Image Card Catalog--Reaping the Benefits of Imaging.

ERIC Educational Resources Information Center

Henthorne, Eileen

1995-01-01

Describes a project at the Princeton University libraries that converted the pre-1981 public card catalog, using digital imaging and optical character recognition technology, to fully tagged and indexed records of text in MARC format that are available on an online database and will be added to the online catalog. (LRW)

The redwood project: An overview

NASA Technical Reports Server (NTRS)

Cheatham, Sam

1993-01-01

Redwood is a new generation tape subsystem now under development at StorageTek using helical scan technology. This library based storage subsystem is designed for the high performance, deep archival market. The topics are presented in viewgraph form and include the following: subsystem overview, media standards, Redwood developed tape, D3 helical recording format, Redwood cartridge, host software for Redwood libraries, and market opportunities.

Library Subject Guides: A Content Management Case Study at the Open University, UK

ERIC Educational Resources Information Center

Wales, Tim

2005-01-01

Purpose: To share the experiences and challenges faced by the Open University Library (OUL) in developing a content management (CM) system for its subject guides. Design/methodology/approach: A summary of multi-format subject guide production at the OUL is provided to justify the decision to develop a new system for their production using a…

An Investigation into the Economics of Retrospective Conversion Using a CD-ROM System.

ERIC Educational Resources Information Center

Co, Francisca K.

This study compares the cost effectiveness of using a CD-ROM (compact disk read-only memory) system known as Bibliofile and the currently used OCLC (Online Computer Library Center)-based method to convert a university library's shelflist into a machine-readable database in the MARC (Machine-Readable Cataloging) format. The cost of each method of…

The Library of Congress: Evaluation of the NLS/BPH Braille and Audio Magazine Program. Final Project Report.

ERIC Educational Resources Information Center

Bosma and Associates International, Seattle, WA.

This final report presents an independent formative and summative evaluation of the National Library Services for the Blind and Physically Handicapped (NLS/BPH) braille and audio magazine program. In this program, 77 magazines are distributed directly to subscribers, with 43 magazines available on audio flexible discs and 34 magazines available in…

Knowing Where They Went: Six Years of Online Access Statistics via the Online Catalog for Federal Government Information

ERIC Educational Resources Information Center

Brown, Christopher C.

2011-01-01

As federal government information is increasingly migrating to online formats, libraries are providing links to this content via URLs or persistent URLs (PURLs) in their online public access catalogs (OPACs). Clickthrough statistics that accumulated as users visited links to online content in the University of Denver's library OPAC were gathered…

Does Your Library's Web Site Pass the Usability Test? Online Treasures

ERIC Educational Resources Information Center

Balas, Janet L.

2005-01-01

In days that seem very long ago, when the card catalog was the only way to search a library's collection, there was very little debate about the usability of the catalog. Librarians were most concerned about properly formatting catalog cards and, of course, ensuring that the cards were filed correctly. Today, the card catalog has been replaced in…

Integrated Platform for Expedited Synthesis–Purification–Testing of Small Molecule Libraries

PubMed Central

2017-01-01

The productivity of medicinal chemistry programs can be significantly increased through the introduction of automation, leading to shortened discovery cycle times. Herein, we describe a platform that consolidates synthesis, purification, quantitation, dissolution, and testing of small molecule libraries. The system was validated through the synthesis and testing of two libraries of binders of polycomb protein EED, and excellent correlation of obtained data with results generated through conventional approaches was observed. The fully automated and integrated platform enables batch-supported compound synthesis based on a broad array of chemical transformations with testing in a variety of biochemical assay formats. A library turnaround time of between 24 and 36 h was achieved, and notably, each library synthesis produces sufficient amounts of compounds for further evaluation in secondary assays thereby contributing significantly to the shortening of medicinal chemistry discovery cycles. PMID:28435537

Curriculum-based neurosurgery digital library.

PubMed

Langevin, Jean-Philippe; Dang, Thai; Kon, David; Sapo, Monica; Batzdorf, Ulrich; Martin, Neil

2010-11-01

Recent work-hour restrictions and the constantly evolving body of knowledge are challenging the current ways of teaching neurosurgery residents. To develop a curriculum-based digital library of multimedia content to face the challenges in neurosurgery education. We used the residency program curriculum developed by the Congress of Neurological Surgeons to structure the library and Microsoft Sharepoint as the user interface. This project led to the creation of a user-friendly and searchable digital library that could be accessed remotely and throughout the hospital, including the operating rooms. The electronic format allows standardization of the content and transformation of the operating room into a classroom. This in turn facilitates the implementation of a curriculum within the training program and improves teaching efficiency. Future work will focus on evaluating the efficacy of the library as a teaching tool for residents.

The IRI/LDEO Climate Data Library: Helping People use Climate Data

NASA Astrophysics Data System (ADS)

Blumenthal, M. B.; Grover-Kopec, E.; Bell, M.; del Corral, J.

2005-12-01

The IRI Climate Data Library (http://iridl.ldeo.columbia.edu/) is a library of datasets. By library we mean a collection of things, collected from both near and far, designed to make them more accessible for the library's users. Our datasets come from many different sources, many different "data cultures", many different formats. By dataset we mean a collection of data organized as multidimensional dependent variables, independent variables, and sub-datasets, along with the metadata (particularly use-metadata) that makes it possible to interpret the data in a meaningful manner. Ingrid, which provides the infrastructure for the Data Library, is an environment that lets one work with datasets: read, write, request, serve, view, select, calculate, transform, ... . It hides an extraordinary amount of technical detail from the user, letting the user think in terms of manipulations to datasets rather that manipulations of files of numbers. Among other things, this hidden technical detail could be accessing data on servers in other places, doing only the small needed portion of an enormous calculation, or translating to and from a variety of formats and between "data cultures". These operations are presented as a collection of virtual directories and documents on a web server, so that an ordinary web client can instantiate a calculation simply by requesting the resulting document or image. Building on this infrastructure, we (and others) have created collections of dynamically-updated images to faciliate monitoring aspects of the climate system, as well as linking these images to the underlying data. We have also created specialized interfaces to address the particular needs of user groups that IRI needs to support.

HepML, an XML-based format for describing simulated data in high energy physics

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

2010-10-01

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces - Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size - 25.0 Kb).

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

The selection performance of an antibody library displayed on filamentous phage coat proteins p9, p3 and truncated p3.

PubMed

Huovinen, Tuomas; Syrjänpää, Markku; Sanmark, Hanna; Seppä, Titta; Akter, Sultana; Khan, Liton Md Ferdhos; Lamminmäki, Urpo

2014-09-19

Filamentous phage display has become an ordinary tool to engineer antibody fragments. Several capsid proteins have been applied for displaying antibodies, of which gene III (p3) protein is used the most followed by experiments with gene IX (p9) protein. Despite the popularity, there are no library scale studies to objectively compare differences in the selection performance of the libraries, when displayed via different capsid proteins. In this study, an identical antibody repertoire was displayed as Fab fragments on p9, p3 and truncated p3 (p3Δ). In addition, the library clones were displayed as ScFv fragments on p3Δ and the Fab-p3 display valency was modulated by hyperphage and VCS-M13 superinfections. The selection performances of the libraries were followed in repeated parallel panning reactions against streptavidin (STR) and digoxigenin (DIG). Selection was successful with all display formats, but the enrichment of specific clones from Fab-p9 library was clearly less efficient than from the other libraries. The most diverse outputs were obtained from p3Δ display and the highest affinity anti-DIG antibodies from the ScFv repertoire. Unfortunately, the number of retrieved specific clones was too low for explicit analysis of the differences in the number of obtained unique clones from each library. However, severe reduction in sequence diversity was observed in p3-Fab libraries prior to panning, which in turn, materialized as a low number of unique specific clones. Oligovalent display by hyperphage resulted in a higher number of unique clones, but the same highest affinity anti-DIG Fab was recovered also by VCS-M13 superinfection. The compromised enrichment of the target-specific clones from the Fab repertoire as a fusion to p9 capsid protein in our experiments, the significant loss of functional diversity in Fab-p3 library after single phage packing cycle and the retrieval of higher affinity anti-digoxigenin clones as ScFv molecules than as Fab molecules from the same source repertoire indicate that the chosen display format may have a significant impact on the selection outcome. This study demonstrates that in addition to library content, also display related issues, should be taken into consideration when planning directed evolution experiments.

New Directions in Assessment: Using Library of Congress Sources to Assess Historical Understanding

ERIC Educational Resources Information Center

Wineburg, Sam; Smith, Mark; Breakstone, Joel

2012-01-01

Research has shown that formative assessment is a key ingredient in raising student achievement. The goal of formative assessment is not to grade students, but to pinpoint where they are having trouble and then to take appropriate instructional action. In a review of 250 studies, Black and Wiliam found that formative assessments had a more…

Teaming to Teach the Information Problem-Solving Process.

ERIC Educational Resources Information Center

Sine, Lynn; Murphy, Becky

1992-01-01

Explains a problem-solving format developed by a school media specialist and first grade teacher that used the framework of Eisenberg and Berkowitz's "Big Six Skills" for library media programs. The application of the format to a science unit on the senses is described. (two references) (MES)

A Step-by-Step Study of Formative Assessment

ERIC Educational Resources Information Center

Pietsch, Laura

2013-01-01

This article presents a guide to the development of formative assessments for school librarians participating in professional learning communities (PLC). It describes librarians' reading of assigned books, meeting with their PLCs, and incorporation of learned strategies in their daily instruction. Central library service readers' regular visits to…

Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

PubMed Central

Bhat, Venugopal T.; Caniard, Anne M.; Luksch, Torsten; Brenk, Ruth; Campopiano, Dominic J.; Greaney, Michael F.

2010-01-01

Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site. PMID:20489719

Bishydrazinium and Diammonium Salts of 4,4’,5,5’-Tetranitro-2,2’-biimidazolate (TNBI): Synthesis and Properties

DTIC Science & Technology

2015-01-01

detonation were all calculated with CHEETAH 6.0 using the exp 6.3 library. The per- formance values as reported for NTO and RDX are provided for comparison...purposes and were generated using the CHEETAH 6.0 reactant library values for heat of formation and density for these materials. 3.2 Synthetic

NOAA Photo Library

Science.gov Websites

- nssl0057 Early stage of tornado formation. Photo #1 of a series of classic photographs of this tornado Available Publication of the U.S. Department of Commerce, National Oceanic & Atmospheric Adminstration NOAA Photo Library Banner Takes you to the Top Page Takes you to the About this Site page. Takes

Do We Still Need Controlled Vocabulary? Of Course, We Do! But How Do We Get It: The Roles for Text Analysis Softwares.

ERIC Educational Resources Information Center

Greenfield, Rich

The author argues that traditional library cataloging (MARC) and the online public access catalog (OPAC) are in collision with the world of the Internet because items in electronic formats undergo MARC cataloging only on a very selective basis. Also the library profession initially isolated itself from World Wide Web development by predicting no…

AST: World Coordinate Systems in Astronomy

NASA Astrophysics Data System (ADS)

Berry, David S.; Warren-Smith, Rodney F.

2014-04-01

The AST library provides a comprehensive range of facilities for attaching world coordinate systems to astronomical data, for retrieving and interpreting that information in a variety of formats, including FITS-WCS, and for generating graphical output based on it. Core projection algorithms are provided by WCSLIB (ascl:1108.003) and astrometry is provided by the PAL (ascl:1606.002) and SOFA (ascl:1403.026) libraries. AST bindings are available in Python (pyast), Java (JNIAST) and Perl (Starlink::AST). AST is used as the plotting and astrometry library in DS9 and GAIA, and is distributed separately and as part of the Starlink software collection.

Fission yield covariances for JEFF: A Bayesian Monte Carlo method

NASA Astrophysics Data System (ADS)

Leray, Olivier; Rochman, Dimitri; Fleming, Michael; Sublet, Jean-Christophe; Koning, Arjan; Vasiliev, Alexander; Ferroukhi, Hakim

2017-09-01

The JEFF library does not contain fission yield covariances, but simply best estimates and uncertainties. This situation is not unique as all libraries are facing this deficiency, firstly due to the lack of a defined format. An alternative approach is to provide a set of random fission yields, themselves reflecting covariance information. In this work, these random files are obtained combining the information from the JEFF library (fission yields and uncertainties) and the theoretical knowledge from the GEF code. Examples of this method are presented for the main actinides together with their impacts on simple burn-up and decay heat calculations.

A Multi-Discipline, Multi-Genre Digital Library for Research and Education

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

2004-01-01

We describe NCSTRL+, a unified, canonical digital library for educational and scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 100 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets". We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information.

CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

PubMed

Duffy, Fergal J; Verniere, Mélanie; Devocelle, Marc; Bernard, Elise; Shields, Denis C; Chubb, Anthony J

2011-04-25

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Interlibrary Loan of Alternative Format Materials: A Balanced Sourcebook.

ERIC Educational Resources Information Center

Massis, Bruce E., Ed.; Vitzansky, Winnie, Ed.

This document presents perspectives on, and a reference guide to internationally interlending materials in alternate formats (recordings, braille, large print). A questionnaire was sent to the world's known libraries serving the blind; results of the survey include specific lending information from 29 countries including: South Africa, Hong Kong,…

Testing of ENDF71x: A new ACE-formatted neutron data library based on ENDF/B-VII.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardiner, S. J.; Conlin, J. L.; Kiedrowski, B. C.

The ENDF71x library [1] is the most thoroughly tested set of ACE-format data tables ever released by the Nuclear Data Team at Los Alamos National Laboratory (LANL). It is based on ENDF/B-VII. 1, the most recently released set of evaluated nuclear data files produced by the US Cross Section Evaluation Working Group (CSEWG). A variety of techniques were used to test and verify the ENDF7 1x library before its public release. These include the use of automated checking codes written by members of the Nuclear Data Team, visual inspections of key neutron data, MCNP6 calculations designed to test data formore » every included combination of isotope and temperature as comprehensively as possible, and direct comparisons between ENDF71x and previous ACE library releases. Visual inspection of some of the most important neutron data revealed energy balance problems and unphysical discontinuities in the cross sections for some nuclides. Doppler broadening of the total cross sections with increasing temperature was found to be qualitatively correct. Test calculations performed using MCNP prompted two modifications to the MCNP6 source code and also exposed bad secondary neutron yields for {sup 231,233}Pa that are present in both ENDF/B-VII.1 and ENDF/B-VII.0. A comparison of ENDF71x with its predecessor ACE library, ENDF70, showed that dramatic changes have been made in the neutron cross section data for a number of isotopes between ENDF/B-VII.0 and ENDF/B-VII.1. Based on the results of these verification tests and the validation tests performed by Kahler, et al. [2], the ENDF71x library is recommended for use in all Monte Carlo applications. (authors)« less

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Transcriptome Analysis of Gene Expression during Chinese Water Chestnut Storage Organ Formation

PubMed Central

Chen, Sainan; Wang, Yan; Yu, Meizhen; Chen, Xuehao; Li, Liangjun; Yin, Jingjing

2016-01-01

The product organ (storage organ; corm) of the Chinese water chestnut has become a very popular food in Asian countries because of its unique nutritional value. Corm formation is a complex biological process, and extensive whole genome analysis of transcripts during corm development has not been carried out. In this study, four corm libraries at different developmental stages were constructed, and gene expression was identified using a high-throughput tag sequencing technique. Approximately 4.9 million tags were sequenced, and 4,371,386, 4,372,602, 4,782,494, and 5,276,540 clean tags, including 119,676, 110,701, 100,089, and 101,239 distinct tags, respectively, were obtained after removal of low-quality tags from each library. More than 39% of the distinct tags were unambiguous and could be mapped to reference genes, while 40% were unambiguous tag-mapped genes. After mapping their functions in existing databases, a total of 11,592, 10,949, 10,585, and 7,111 genes were annotated from the B1, B2, B3, and B4 libraries, respectively. Analysis of the differentially expressed genes (DEGs) in B1/B2, B2/B3, and B3/B4 libraries showed that most of the DEGs at the B1/B2 stages were involved in carbohydrate and hormone metabolism, while the majority of DEGs were involved in energy metabolism and carbohydrate metabolism at the B2/B3 and B3/B4 stages. All of the upregulated transcription factors and 9 important genes related to product organ formation in the above four stages were also identified. The expression changes of nine of the identified DEGs were validated using a quantitative PCR approach. This study provides a comprehensive understanding of gene expression during corm formation in the Chinese water chestnut. PMID:27716802

An Overview of the Project on the Imaging and Full-Text Retrieval of the Ava Helen and Linus Pauling Papers at the Oregon State University Libraries.

ERIC Educational Resources Information Center

Krishnamurthy, Ramesh S.; Mead, Clifford S.

1995-01-01

Presents plan of Oregon State University Libraries to convert all paper documents from the Ava Helen and Linus Pauling archives to digital format. The scope, goals, tasks and objectives set by the project coordinators are outlined, and issues such as protection of equipment, access, copyright and management are discussed. (JKP)

Ballastic signature identification systems study

NASA Technical Reports Server (NTRS)

Reich, A.; Hine, T. L.

1976-01-01

The results are described of an attempt to establish a uniform procedure for documenting (recording) expended bullet signatures as effortlessly as possible and to build a comprehensive library of these signatures in a form that will permit the automated comparison of a new suspect bullet with the prestored library. The ultimate objective is to achieve a standardized format that will permit nationwide interaction between police departments, crime laboratories, and other interested law enforcement agencies.

Library instruction in medical education: a survey of current practices in the United States and Canada.

PubMed

Nevius, Amanda M; Ettien, A'Llyn; Link, Alissa P; Sobel, Laura Y

2018-01-01

The most recent survey on instruction practices in libraries affiliated with accredited medical institutions in the United States was conducted in 1996. The present study sought to update these data, while expanding to include Canadian libraries. Additional analysis was undertaken to test for statistically significant differences between library instruction in the United States and Canada and between libraries affiliated with highly ranked and unranked institutions. A twenty-eight-question survey was distributed to libraries affiliated with accredited US and Canadian medical schools to assess what and how often librarians teach, as well as how librarians are involved in the curriculum committee and if they are satisfied with their contact with students and faculty. Quantitative data were analyzed with SAS, R, and MedCalc. Most of the seventy-three responding libraries provided instruction, both asynchronously and synchronously. Library instruction was most likely to be offered in two years of medical school, with year one seeing the most activity. Database use was the most frequently taught topic, and libraries reported a median of five librarians providing instruction, with larger staffs offering slightly more education sessions per year. Libraries associated with highly ranked schools were slightly more likely to offer sessions that were integrated into the medical school curriculum in year four and to offer sessions in more years overall. In US and Canadian libraries, regardless of the rank of the affiliated medical school, librarians' provision of instruction in multiple formats on multiple topics is increasingly common.

LC-MS-Based Lipidomics and Automated Identification of Lipids Using the LipidBlast In-Silico MS/MS Library.

PubMed

Cajka, Tomas; Fiehn, Oliver

2017-01-01

This protocol describes the analysis, specifically the identification, of blood plasma lipids. Plasma lipids are extracted using methyl tert-butyl ether (MTBE), methanol, and water followed by separation and data acquisition of isolated lipids using reversed-phase liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry (RPLC-QTOFMS) operated in MS/MS mode. For lipid identification, acquired MS/MS spectra are converted to the mascot generic format (MGF) followed by library search using the in-silico MS/MS library LipidBlast. Using this approach, lipid classes, carbon-chain lengths, and degree of unsaturation of fatty-acid components are annotated.

Report of the IAU Commission 4 Working Group on Standardizing Access to Ephemerides and File Format Specification

DTIC Science & Technology

2014-12-01

format for the orientation of a body. It further recommends support- ing data be stored in a text PCK. These formats are used by the SPICE system...INTRODUCTION These file formats were developed for and are used by the SPICE system, developed by the Navigation and Ancillary Information Facility (NAIF...of NASA’s Jet Propulsion Laboratory (JPL). Most users will want to use either the SPICE libraries or CALCEPH, developed by the Institut de mécanique

Group Constants Generation of the Pseudo Fission Products for Fast Reactor Burnup Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gil, Choong-Sup; Kim, Do Heon; Chang, Jonghwa

The pseudo fission products for the burnup calculations of the liquid metal fast reactor were generated. The cross-section data and fission product yield data of ENDF/B-VI were used for the pseudo fission product data of U-235, U-238, Pu-239, Pu-240, Pu-241, and Pu-242. The pseudo fission product data can be used with the KAFAX-F22 or -E66, which are the MATXS-format libraries for analyses of the liquid metal fast reactor at KAERI and were distributed through the OECD/NEA. The 80-group MATXS-format libraries of the 172 fission products were generated and the burnup chains for generation of the pseudo fission products were prepared.

RT11LIB: a library of subroutines for transferring data between a PDP-11 and CDC-6600

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, H.D.

1978-01-01

RT11LIB is a library of subroutines available to CDC 6600 users for the purpose of transferring data or program listings between a PDP-11 and a CDC 6600. These subroutines, operating on a CDC 6600 under the NOS/BE or SCOPE 3.4 operating systems, read or write magnetic tapes that are compatible with the PDP-11's RT11 operating system. Data written on the tape by the PDP-11 can be read by these subroutines and then translated into CDC 6600 format for subsequent data analysis. The translation process provides for many data formats, including byte, integer, floating point, and character string formats. Alternatively, datamore » from the CDC 6600 can be translated into PDP-11 format then written onto the tape for subsequent use on the PDP-11. This facility allows a program punched on a card deck by a keypunch operator to be transferred to the PDP-11, even though the PDP-11 is not itself equipped with a card reader.« less

Chapter 21: Programmatic Interfaces - STILTS

NASA Astrophysics Data System (ADS)

Fitzpatrick, M. J.

STILTS is the Starlink Tables Infrastructure Library Tool Set developed by Mark Taylor of the former Starlink Project. STILTS is a command-line tool (see the NVOSS_HOME/bin/stilts command) providing access to the same functionality driving the TOPCAT application and can be run using either the STILTS-specific jar file, or the more general TOPCAT jar file (both are available in the NVOSS_HOME/java/lib directory and are included in the default software environment classpath). The heart of both STILTS and TOPCAT is the STIL Java library. STIL is designed to efficiently handle the input, output and processing of very large tabular datasets and the STILTS task interface makes it an ideal tool for the scripting environment. Multiple formats are supported (including FITS Binary Tables, VOTable, CSV, SQL databases and ASCII, amongst others) and while some tools will generically handle all supported formats, others are specific to the VOTable format. Converting a VOTable to a more script-friendly format is the first thing most users will encounter, but there are many other useful tools as well.

Implementing the HDF-EOS5 software library for data products in the UNAVCO InSAR archive

NASA Astrophysics Data System (ADS)

Baker, Scott; Meertens, Charles; Crosby, Christopher

2017-04-01

UNAVCO is a non-profit university-governed consortium that operates the U.S. National Science Foundation (NSF) Geodesy Advancing Geosciences and EarthScope (GAGE) facility and provides operational support to the Western North America InSAR Consortium (WInSAR). The seamless synthetic aperture radar archive (SSARA) is a seamless distributed access system for SAR data and higher-level data products. Under the NASA-funded SSARA project, a user-contributed InSAR archive for interferograms, time series, and other derived data products was developed at UNAVCO. The InSAR archive development has led to the adoption of the HDF-EOS5 data model, file format, and library. The HDF-EOS software library was designed to support NASA Earth Observation System (EOS) science data products and provides data structures for radar geometry (Swath) and geocoded (Grid) data based on the HDF5 data model and file format provided by the HDF Group. HDF-EOS5 inherits the benefits of HDF5 (open-source software support, internal compression, portability, support for structural data, self-describing file metadata enhanced performance, and xml support) and provides a way to standardize InSAR data products. Instrument- and datatype-independent services, such as subsetting, can be applied to files across a wide variety of data products through the same library interface. The library allows integration with GIS software packages such as ArcGIS and GDAL, conversion to other data formats like NetCDF and GeoTIFF, and is extensible with new data structures to support future requirements. UNAVCO maintains a GitHub repository that provides example software for creating data products from popular InSAR processing software packages like GMT5SAR and ISCE as well as examples for reading and converting the data products into other formats. Digital object identifiers (DOI) have been incorporated into the InSAR archive allowing users to assign a permanent location for their processed result and easily reference the final data products. A metadata attribute is added to the HDF-EOS5 file when a DOI is minted for a data product. These data products are searchable through the SSARA federated query providing access to processed data for both expert and non-expert InSAR users. The archive facilitates timely distribution of processed data with particular importance for geohazards and event response.

Generation of an arrayed CRISPR-Cas9 library targeting epigenetic regulators: from high-content screens to in vivo assays

PubMed Central

2017-01-01

ABSTRACT The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Screens employing genome-scale pooled small guide RNA (sgRNA) libraries are demanding, particularly when complex assays are used. Furthermore, pooled libraries are not suitable for microscopy-based high-content screens or for systematic interrogation of protein function. To overcome these limitations and exploit CRISPR-based technologies to comprehensively investigate epigenetic mechanisms, we have generated a focused sgRNA library targeting 450 epigenetic regulators with multiple sgRNAs in human cells. The lentiviral library is available both in an arrayed and pooled format and allows temporally-controlled induction of gene knock-out. Characterization of the library showed high editing activity of most sgRNAs and efficient knock-out at the protein level in polyclonal populations. The sgRNA library can be used for both selection and high-content screens, as well as for targeted investigation of selected proteins without requiring isolation of knock-out clones. Using a variety of functional assays we show that the library is suitable for both in vitro and in vivo applications, representing a unique resource to study epigenetic mechanisms in physiological and pathological conditions. PMID:29327641

Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library.

PubMed

Chen, Shiuan; Hsieh, Jui-Hua; Huang, Ruili; Sakamuru, Srilatha; Hsin, Li-Yu; Xia, Menghang; Shockley, Keith R; Auerbach, Scott; Kanaya, Noriko; Lu, Hannah; Svoboda, Daniel; Witt, Kristine L; Merrick, B Alex; Teng, Christina T; Tice, Raymond R

2015-10-01

Multiple mechanisms exist for endocrine disruption; one nonreceptor-mediated mechanism is via effects on aromatase, an enzyme critical for maintaining the normal in vivo balance of androgens and estrogens. We adapted the AroER tri-screen 96-well assay to 1536-well format to identify potential aromatase inhibitors (AIs) in the U.S. Tox21 10K compound library. In this assay, screening with compound alone identifies estrogen receptor alpha (ERα) agonists, screening in the presence of testosterone (T) identifies AIs and/or ERα antagonists, and screening in the presence of 17β-estradiol (E2) identifies ERα antagonists. Screening the Tox-21 library in the presence of T resulted in finding 302 potential AIs. These compounds, along with 31 known AI actives and inactives, were rescreened using all 3 assay formats. Of the 333 compounds tested, 113 (34%; 63 actives, 50 marginal actives) were considered to be potential AIs independent of cytotoxicity and ER antagonism activity. Structure-activity analysis suggested the presence of both conventional (eg, 1, 2, 4, - triazole class) and novel AI structures. Due to their novel structures, 14 of the 63 potential AI actives, including both drugs and fungicides, were selected for confirmation in the biochemical tritiated water-release aromatase assay. Ten compounds were active in the assay; the remaining 4 were only active in high-throughput screen assay, but with low efficacy. To further characterize these 10 novel AIs, we investigated their binding characteristics. The AroER tri-screen, in high-throughput format, accurately and efficiently identified chemicals in a large and diverse chemical library that selectively interact with aromatase. © The Author 2015. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library

PubMed Central

Chen, Shiuan; Hsieh, Jui-Hua; Huang, Ruili; Sakamuru, Srilatha; Hsin, Li-Yu; Xia, Menghang; Shockley, Keith R.; Auerbach, Scott; Kanaya, Noriko; Lu, Hannah; Svoboda, Daniel; Witt, Kristine L.; Merrick, B. Alex; Teng, Christina T.; Tice, Raymond R.

2015-01-01

Multiple mechanisms exist for endocrine disruption; one nonreceptor-mediated mechanism is via effects on aromatase, an enzyme critical for maintaining the normal in vivo balance of androgens and estrogens. We adapted the AroER tri-screen 96-well assay to 1536-well format to identify potential aromatase inhibitors (AIs) in the U.S. Tox21 10K compound library. In this assay, screening with compound alone identifies estrogen receptor alpha (ERα) agonists, screening in the presence of testosterone (T) identifies AIs and/or ERα antagonists, and screening in the presence of 17β-estradiol (E2) identifies ERα antagonists. Screening the Tox-21 library in the presence of T resulted in finding 302 potential AIs. These compounds, along with 31 known AI actives and inactives, were rescreened using all 3 assay formats. Of the 333 compounds tested, 113 (34%; 63 actives, 50 marginal actives) were considered to be potential AIs independent of cytotoxicity and ER antagonism activity. Structure-activity analysis suggested the presence of both conventional (eg, 1, 2, 4, - triazole class) and novel AI structures. Due to their novel structures, 14 of the 63 potential AI actives, including both drugs and fungicides, were selected for confirmation in the biochemical tritiated water-release aromatase assay. Ten compounds were active in the assay; the remaining 4 were only active in high-throughput screen assay, but with low efficacy. To further characterize these 10 novel AIs, we investigated their binding characteristics. The AroER tri-screen, in high-throughput format, accurately and efficiently identified chemicals in a large and diverse chemical library that selectively interact with aromatase. PMID:26141389

Defining Our Role in a Changing World: What Is America, and What Do We Want It To Be? Library Reader 1995. Choices for the 21st Century Education Library Series.

ERIC Educational Resources Information Center

Brown Univ., Providence, RI. Thomas J. Watson, Jr. Inst. for International Studies.

This reader provides background information for a public policy discussion program about the nation's future at this critical point in history. Through a non-partisan discussion format, citizens are encouraged to deliberate about the direction in which the nation should head in the years to come. This reader employs a multi-disciplinary approach…

The Development and Implementation of a Minimum Objective System in the Hinesburg Elementary School. Hinesburg Elementary School Minimum Objectives for Science, Physical Education, Music, Library. Appendix B: Vol. 3.

ERIC Educational Resources Information Center

Morse, Margaret; And Others

The appendix to the report of the minimum objective system of the Hinesburg Elementary School (Vermont) includes objectives for science, physical education, music, and library skills, from the kindergarten through grade 6 levels. Most objectives are presented in the format of condition (or task), student behavior, and criteria. Also included are…

Component, Context and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2013-03-01

Penn State team were stored in a relational database for easy access, storage and maintainability. The relational database consisted of a PostGres ...file into a format that can be imported into the PostGres database. This same custom application was used to generate Microsoft Excel templates...Press Break Forming Equipment 4.14 Manufacturing Model Library Database Structure The data storage mechanism for the ARL PSU MML was a PostGres database

Improving Seismic Data Accessibility and Performance Using HDF Containers

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Wang, J.; Yang, R.

2017-12-01

The performance of computational geophysical data processing and forward modelling relies on both computational and data. Significant efforts on developing new data formats and libraries have been made the community, such as IRIS/PASSCAL and ASDF in data, and programs and utilities such as ObsPy and SPECFEM. The National Computational Infrastructure hosts a national significant geophysical data collection that is co-located with a high performance computing facility and provides an opportunity to investigate how to improve the data formats from both a data management and a performance point of view. This paper investigates how to enhance the data usability in several perspectives: 1) propose a convention for the seismic (both active and passive) community to improve the data accessibility and interoperability; 2) recommend the convention used in the HDF container when data is made available in PH5 or ASDF formats; 3) provide tools to convert between various seismic data formats; 4) provide performance benchmark cases using ObsPy library and SPECFEM3D to demonstrate how different data organization in terms of chunking size and compression impact on the performance by comparing new data formats, such as PH5 and ASDF to traditional formats such as SEGY, SEED, SAC, etc. In this work we apply our knowledge and experience on data standards and conventions, such as CF and ACDD from the climate community to the seismology community. The generic global attributes widely used in climate community are combined with the existing convention in the seismology community, such as CMT and QuakeML, StationXML, SEGY header convention. We also extend such convention by including the provenance and benchmarking records so that the r user can learn the footprint of the data together with its baseline performance. In practise we convert the example wide angle reflection seismic data from SEGY to PH5 or ASDF by using ObsPy and pyasdf libraries. It quantitatively demonstrates how the accessibility can be improved if the seismic data are stored in the HDF container.

StrBioLib: a Java library for development of custom computationalstructural biology applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less

StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry.

PubMed

Nour, Hany F; Islam, Tuhidul; Fernández-Lahore, Marcelo; Kuhnert, Nikolai

2012-12-30

Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest. Copyright © 2012 John Wiley & Sons, Ltd.

Razzle Dazzle Reading Circus: A Bibliography of Books in Recorded and Braille Formats for Young Readers from Preschool through Junior High. Silver Summer Scrapbook--Summer Library Program, 1993.

ERIC Educational Resources Information Center

Sumner, Mary Ann, Comp.

This annotated bibliography comprises an alphabetical listing of 34 books on circuses available in special formats. The list has books about true circus stories; make believe stories; and circus animals. The reading levels of the books range from preschool through junior high school. Formats included in the bibliography are cassette books; braille…

Hierachical Data Format 5 v1.10

DOE Office of Scientific and Technical Information (OSTI.GOV)

KOZIOL, QUINCEY

2016-04-20

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

Library instruction in medical education: a survey of current practices in the United States and Canada

PubMed Central

Nevius, Amanda M.; Ettien, A’Llyn; Link, Alissa P.; Sobel, Laura Y.

2018-01-01

Objective The most recent survey on instruction practices in libraries affiliated with accredited medical institutions in the United States was conducted in 1996. The present study sought to update these data, while expanding to include Canadian libraries. Additional analysis was undertaken to test for statistically significant differences between library instruction in the United States and Canada and between libraries affiliated with highly ranked and unranked institutions. Methods A twenty-eight-question survey was distributed to libraries affiliated with accredited US and Canadian medical schools to assess what and how often librarians teach, as well as how librarians are involved in the curriculum committee and if they are satisfied with their contact with students and faculty. Quantitative data were analyzed with SAS, R, and MedCalc. Results Most of the seventy-three responding libraries provided instruction, both asynchronously and synchronously. Library instruction was most likely to be offered in two years of medical school, with year one seeing the most activity. Database use was the most frequently taught topic, and libraries reported a median of five librarians providing instruction, with larger staffs offering slightly more education sessions per year. Libraries associated with highly ranked schools were slightly more likely to offer sessions that were integrated into the medical school curriculum in year four and to offer sessions in more years overall. Conclusions In US and Canadian libraries, regardless of the rank of the affiliated medical school, librarians’ provision of instruction in multiple formats on multiple topics is increasingly common. PMID:29339939

Spontaneous self-assembly of a giant spherical metal-oxide Keplerate: addition of one building block induces "immediate" formation of the complementary one from a constitutional dynamic library.

PubMed

Schäffer, Christian; Todea, Ana Maria; Gouzerh, Pierre; Müller, Achim

2012-01-11

The addition of dinuclear {Mo(2)} units to a dynamic library containing molybdates results in the spontaneous self-assembly of a giant spherical metal-oxide species of the type {(Mo)Mo(5)}(12){Mo(2)}(30) while the required pentagonal {(Mo)Mo(5)} building blocks are "immediately" formed. This journal is © The Royal Society of Chemistry 2012

VO-compliant libraries of high resolution spectra of cool stars

NASA Astrophysics Data System (ADS)

Montes, D.

2008-10-01

In this contribution we describe a Virtual Observatory (VO) compliant version of the libraries of high resolution spectra of cool stars described by Montes et al. (1997; 1998; and 1999). Since their publication the fully reduced spectra in FITS format have been available via ftp and in the World Wide Web. However, in the VO all the spectra will be accessible using a common web interface following the standards of the International Virtual Observatory Alliance (IVOA). These libraries include F, G, K and M field stars, from dwarfs to giants. The spectral coverage is from 3800 to 10000 Å, with spectral resolution ranging from 0.09 to 3.0 Å.

Documentation for the machine-readable version of A Library of Stellar Spectra (Jacoby, Hunter and Christian 1984)

NASA Technical Reports Server (NTRS)

Warren, W. H., Jr.

1984-01-01

The machine readable library as it is currently being distributed from the Astronomical Data Center is described. The library contains digital spectral for 161 stars of spectral classes O through M and luminosity classes 1, 3 and 5 in the wavelength range 3510 A to 7427 A. The resolution is approximately 4.5 A, while the typical photometric uncertainty of each resolution element is approximately 1 percent and broadband variations are 3 percent. The documentation includes a format description, a table of the indigenous characteristics of the magnetic tape file, and a sample listing of logical records exactly as they are recorded on the tape.

Proceedings of Colloquium 110 of the International Astronomical Union on Library and Information Services in Astronomy

NASA Astrophysics Data System (ADS)

Wilkins, George A.; Stevens-Rayburn, Sarah

This report provides an overview of the presentations and summaries of discussions at IAU Colloquium 110, which was held in Washington, D.C., on 26-30 July 1988 and at the Goddard Space Flight Center on 1 August 1988. The topics included: the publication and acquisition of books and journals; searching for astronomical information; the handling and use of special-format materials; conservation; archiving of unpublished documents; uses of computers in libraries; astronomical databases and various aspects of the administration of astronomy libraries and services. Particular attention was paid to new developments, but the problems of astronomers and institutions in developing countries were also considered.

Library & Information Services: an Astronomer's Wishlist

NASA Astrophysics Data System (ADS)

Andernach, Heinz

I review some of the past and current methods for retrieval of literature and other published information, excluding commercial services. Much of this is a personal view and based on experience made at various institutions, some of them neither with an adequately complete astronomy library, nor with a professional astronomy librarian. Rather than describing current retrieval methods, a few of their weaknesses are identified which merit future improval. Despite the availability of powerful electronic tools, we need to improve efforts in safeguarding published numerical and textual information in a format readily usable by astronomers. Comments are made on a user-friendly arrangement of a library, and on useful tasks for librarians with available time.

Open Babel: An open chemical toolbox

PubMed Central

2011-01-01

Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

Development and implementation of an electronic library tour for the NASA Langley Technical Library. M.S. Thesis, North Carolina Univ., Jul. 1994

NASA Technical Reports Server (NTRS)

Rinker, Nancy A.

1994-01-01

The role of librarians today is drastically influenced by the changing nature of information and library services. The museum-like libraries of yesterday are a thing of the past: today's libraries are bustling with life, activity, and the sounds of new technologies. Libraries are replacing their paper card catalogs with state-of-the-art online systems, which provide faster and more comprehensive search capabilities. Even the resources themselves are changing. New formats for information, such as CD-ROM's, are becoming popular for all types of publications, from bibliographic tools to encyclopedias to electronic journals, even replacing print materials completely in some cases. Today it is almost impossible to walk into a library and find the information you need without coming into contact with at least one computer system. Librarians are not only struggling to keep up with the technological advancements of the day, but they are becoming information intermediaries: they must teach library users how to use all of the new systems and electronic resources. Not surprisingly, bibliographic instruction itself has taken on a new look and feel in these electronically advanced libraries. Many libraries are experimenting with the development of expert systems and other computer aided instruction interfaces for teaching patrons how to use the library and its resources. One popular type of interface in library instruction programs is hypertext, which utilizes 'stacks' or linked pages of information. Hypertext stacks can incorporate color graphics along with text to provide a more interesting interface and entice users into trying out the system. Another advantage of hypertext is that it is generally easy to use, even for those unfamiliar with computers. As such, it lends itself well to application in libraries, which often serve a broad range of clientele. This paper will discuss the design, development, and implementation of a hypertext library tour in a special library setting. The library featured in the electronic library tour is the National Aeronautics and Space Administration's Technical Library at Langley Research Center in Hampton, Virginia.

ANSL-V: ENDF/B-V based multigroup cross-section libraries for Advanced Neutron Source (ANS) reactor studies. Supplement 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, R.Q.; Renier, J.P.; Bucholz, J.A.

1995-08-01

The original ANSL-V cross-section libraries (ORNL-6618) were developed over a period of several years for the physics analysis of the ANS reactor, with little thought toward including the materials commonly needed for shielding applications. Materials commonly used for shielding applications include calcium barium, sulfur, phosphorous, and bismuth. These materials, as well as {sup 6}Li, {sup 7}Li, and the naturally occurring isotopes of hafnium, have been added to the ANSL-V libraries. The gamma-ray production and gamma-ray interaction cross sections were completely regenerated for the ANSL-V 99n/44g library which did not exist previously. The MALOCS module was used to collapse the 99n/44gmore » coupled library to the 39n/44g broad- group library. COMET was used to renormalize the two-dimensional (2- D) neutron matrix sums to agree with the one-dimensional (1-D) averaged values. The FRESH module was used to adjust the thermal scattering matrices on the 99n/44g and 39n/44g ANSL-V libraries. PERFUME was used to correct the original XLACS Legendre polynomial fits to produce acceptable distributions. The final ANSL-V 99n/44g and 39n/44g cross-section libraries were both checked by running RADE. The AIM module was used to convert the master cross-section libraries from binary coded decimal to binary format (or vice versa).« less

Citation analysis of Minnesota Department of Health official publications and journal articles: a needs assessment for the RN Barr Library.

PubMed

Rethlefsen, Melissa L

2007-07-01

The paper describes the information needs of a state public health agency, compares needs to its library's collection, and evaluates collection development policy accordingly. A citation analysis of journal articles authored by Minnesota Department of Health staff as well as official publications from 2002 to 2004 was conducted. Fifty-six publications fitting the criteria for inclusion in the study were identified using PubMed and library records. Information on each cited reference was recorded, including reference type, relative age of citation, and journal name, if applicable. The library's collection and collection development policies were analyzed in regard to the results. As expected, journals were the most heavily cited format: 63% (n = 897) of all citations were to journal articles. Most cited materials were between 2 and 5 years old. The 897 journal citations represented 265 different journals. The top 10 cited journals (4% of all titles) accounted for 36% (n = 320) of all citations; 62% (n = 320) of journals were cited only once. Of the total journals cited, the library subscribed to 70% (n = 627). Overall, no large gaps appeared in the RN Barr Library's journal collection. The analysis confirms that the library's collections budget for serials and books reflects the cited use of these materials.

Fifteen hundred guidelines and growing: the UK database of clinical guidelines.

PubMed

van Loo, John; Leonard, Niamh

2006-06-01

The National Library for Health offers a comprehensive searchable database of nationally approved clinical guidelines, called the Guidelines Finder. This resource, commissioned in 2002, is managed and developed by the University of Sheffield Health Sciences Library. The authors introduce the historical and political dimension of guidelines and the nature of guidelines as a mechanism to ensure clinical effectiveness in practice. The article then outlines the maintenance and organisation of the Guidelines Finder database itself, the criteria for selection, who publishes guidelines and guideline formats, usage of the Guidelines Finder service and finally looks at some lessons learnt from a local library offering a national service. Clinical guidelines are central to effective clinical practice at the national, organisational and individual level. The Guidelines Finder is one of the most visited resources within the National Library for Health and is successful in answering information needs related to specific patient care, clinical research, guideline development and education.

The PDA as a reference tool: libraries' role in enhancing nursing education.

PubMed

Scollin, Patrick; Callahan, John; Mehta, Apurva; Garcia, Elizabeth

2006-01-01

"The PDA as a Reference Tool: The Libraries' Role in Enhancing Nursing Education" is a pilot project funded by the University of Massachusetts President's Office Information Technology Council through their Professional Development Grant program in 2004. The project's goal is to offer faculty and students in nursing programs at two University of Massachusetts campuses access to an array of medical reference information, such as handbooks, dictionaries, calculators, and diagnostic tools, on small handheld computers called personal digital assistants. Through exposure to the variety of information resources in this digital format, participants can discover and explore these resources at no personal financial cost. Participants borrow handhelds from the University Library's circulation desks. The libraries provide support in routine resynchronizing of handhelds to update information. This report will discuss how the projects were administered, what we learned about what did and did not work, the problems and solutions, and where we hope to go from here.

Libraries of High and Mid-Resolution Spectra of F, G, K, and M Field Stars

NASA Astrophysics Data System (ADS)

Montes, D.

1998-06-01

I have compiled here the three libraries of high and mid-resolution optical spectra of late-type stars I have recently published. The libraries include F, G, K and M field stars, from dwarfs to giants. The spectral coverage is from 3800 to 1000 Å, with spectral resolution ranging from 0.09 to 3.0 Å. These spectra include many of the spectral lines most widely used as optical and near-infrared indicators of chromospheric activity. The spectra have been obtained with the aim of providing a library of high and mid-resolution spectra to be used in the study of active chromosphere stars by applying a spectral subtraction technique. However, the data set presented here can also be utilized in a wide variety of ways. A digital version of all the fully reduced spectra is available via FTP and the World Wide Web (WWW) in FITS format.

CGNS Mid-Level Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Poirier, Diane; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: - The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media; - The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; - The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and - The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The CGNS Mid-level Library was designed to ease the implementation of CGNS by providing developers with a collection of handy I/O functions. Since knowledge of the ADF core is not required to use this library, it will greatly facilitate the task of interfacing with CGNS. There are currently 48 user callable functions that comprise the Mid-level library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Customizing for clients: developing a library liaison program from need to plan.

PubMed

Tennant, M R; Butson, L C; Rezeau, M E; Tucker, P J; Boyle, M E; Clayton, G

2001-01-01

Building on the experiences of librarian representatives to curriculum committees in the colleges of dentistry, medicine, and nursing, the Health Science Center Libraries (HSCL) Strategic Plan recommended the formation of a Library Liaison Work Group to create a formal Library Liaison Program to serve the six Health Science Center (HSC) colleges and several affiliated centers and institutes. The work group's charge was to define the purpose and scope of the program, identify models of best practice, and recommend activities for liaisons. The work group gathered background information, performed an environmental scan, and developed a philosophy statement, a program of liaison activities focusing on seven primary areas, and a forum for liaison communication. Hallmarks of the plan included intensive subject specialization (beyond collection development), extensive communication with users, and personal information services. Specialization was expected to promote competence, communication, confidence, comfort, and customization. Development of the program required close coordination with other strategic plan implementation teams, including teams for collection development, education, and marketing. This paper discusses the HSCL's planning process and the resulting Library Liaison Program. Although focusing on an academic health center, the planning process and liaison model may be applied to any library serving diverse, subject-specific user populations.

Customizing for clients: developing a library liaison program from need to plan*

PubMed Central

Tennant, Michele R.; Butson, Linda C.; Rezeau, Michelle E.; Tucker, Prudence J.; Boyle, Marian E.; Clayton, Greg

2001-01-01

Building on the experiences of librarian representatives to curriculum committees in the colleges of dentistry, medicine, and nursing, the Health Science Center Libraries (HSCL) Strategic Plan recommended the formation of a Library Liaison Work Group to create a formal Library Liaison Program to serve the six Health Science Center (HSC) colleges and several affiliated centers and institutes. The work group's charge was to define the purpose and scope of the program, identify models of best practice, and recommend activities for liaisons. The work group gathered background information, performed an environmental scan, and developed a philosophy statement, a program of liaison activities focusing on seven |primary areas, and a forum for liaison communication. Hallmarks of the plan included intensive subject specialization (beyond collection development), extensive communication with users, and personal information services. Specialization was expected to promote competence, communication, confidence, comfort, and customization. Development of the program required close coordination with other strategic plan implementation teams, including teams for collection development, education, and marketing. This paper discusses the HSCL's planning process and the resulting Library Liaison Program. Although focusing on an academic health center, the planning process and liaison model may be applied to any library serving diverse, subject-specific user populations. PMID:11209807

Lunar e-Library: Putting Space History to Work

NASA Technical Reports Server (NTRS)

McMahan, Tracy A.; Shea, Charlotte A.; Finckenor, Miria

2006-01-01

As NASA plans and implements the Vision for Space Exploration, managers, engineers, and scientists need historically important information that is readily available and easily accessed. The Lunar e-Library - a searchable collection of 1100 electronic (.PDF) documents - makes it easy to find critical technical data and lessons learned and put space history knowledge in action. The Lunar e-Library, a DVD knowledge database, was developed by NASA to shorten research time and put knowledge at users' fingertips. Funded by NASA's Space Environments and Effects (SEE) Program headquartered at Marshall Space Flight Center (MSFC) and the MSFC Materials and Processes Laboratory, the goal of the Lunar e- Library effort was to identify key lessons learned from Apollo and other lunar programs and missions and to provide technical information from those programs in an easy-to-use format. The SEE Program began distributing the Lunar e-Library knowledge database in 2006. This paper describes the Lunar e-Library development process (including a description of the databases and resources used to acquire the documents) and the contents of the DVD product, demonstrates its usefulness with focused searches, and provides information on how to obtain this free resource.

Universal Number Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lloyd, G. Scott

This floating-point arithmetic library contains a software implementation of Universal Numbers (unums) as described by John Gustafson [1]. The unum format is a superset of IEEE 754 floating point with several advantages. Computing with unums provides more accurate answers without rounding errors, underflow or overflow. In contrast to fixed-sized IEEE numbers, a variable number of bits can be used to encode unums. This all allows number with only a few significant digits or with a small dynamic range to be represented more compactly.

Getting on the fast track, or how to get an MLIS through distance education, with a specialization in medical librarianship.

PubMed

Detlefsen, Ellen G

2004-01-01

The article describes an innovation in MLIS education for medical librarianship, with an introduction to the FastTrack, the distance education program at the University of Pittsburgh's library and information science school, together with an overview of a model program linking the biomedical library at Vanderbilt University with the School of Information Sciences in Pittsburgh. Admissions requirements and specific curriculum for the distance education master's degree are detailed in an FAQ format.

Studies of asymmetric styrene cyclopropanation with a rhodium(II) metallopeptide catalyst developed with a high-throughput screen.

PubMed

Sambasivan, Ramya; Ball, Zachary T

2013-09-01

Dirhodium metallopeptides have been developed as selective catalysts for asymmetric cyclopropanation reactions. A selective ligand sequence has been identified by screening on-bead metallopeptide libraries in a 96-well plate format. Efficient ligand synthesis and screening allows a 200-member library to be created and assayed in less than three weeks. These metallopeptides catalyze efficient cyclopropanation of aryldiazoacetates, providing asymmetric access to cyclopropane products in high diastereoselectivity. © 2013 Wiley Periodicals, Inc.

IFLA General Conference, 1989. Division of Management and Technology. Section on Conservation; Section on Information Technology; Section on Library Buildings and Equipment; Section on Statistics; Round Table on Audiovisual Media; Round Table for the Management of Library Associations. Booklet 60.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

There are 15 papers in this collection from the Division of Management and Technology: (1) "Les Activites de formation dans les centres regionaux du Programme PAC" (Training Activities in the Regional Centers of the Preservation and Conservation Program) (Jean-Marie Arnoult); (2) "Professional Education for Preservation: An Overview" (John…

Writing Pictures K-12: A Bridge to Writing Workshop. The Bill Harp Professional Teachers Library Series.

ERIC Educational Resources Information Center

Takenishi, Michelle; Takenishi, Hal

This book describes "Writing Pictures," a daily developmental writing exercise in which students visualize a moment in their life of their own choosing, sketch it quickly, and write four guided sentences in paragraph format about it. Beginning with level one, it takes students through the basic format, and, with time, students progress upward…

Land Treatment Digital Library

USGS Publications Warehouse

Pilliod, David S.

2009-01-01

Across the country, public land managers make hundreds of decisions each year that influence landscapes and ecosystems within the lands they manage. Many of these decisions involve vegetation manipulations known as land treatments. Land treatments include activities such as removal or alteration of plant biomass, seeding burned areas, and herbicide applications. Data on these land treatments are usually stored at local offices, and gathering information across large spatial areas can be difficult. There is a need to centralize and store treatment data for Federal agencies involved in land treatments because these data are useful to land managers for policy and management and to scientists for developing sampling designs and studies. The Land Treatment Digital Library (LTDL) was created by the U.S. Geological Survey (USGS) to catalog information about land treatments on Federal lands in the western United States for all interested parties. The flexible framework of the library allows for the storage of a wide variety of data in different formats. The LTDL currently stores previously established land treatments or what often are called legacy data. The project was developed and has been refined based on feedback from partner agencies and stakeholders, with opportunity for the library holdings to expand as new information becomes available. The library contains data in text, tabular, spatial, and image formats. Specific examples include project plans and implementation reports, monitoring data, spatial data files from geographic information systems, digitized paper maps, and digital images of land treatments. The data are entered by USGS employees and are accessible through a searchable web site. The LTDL can be used to respond to information requests, conduct analyses and other forms of information syntheses, produce maps, and generate reports for DOI managers and scientists and other authorized users.

An efficient strategy for cell-based antibody library selection using an integrated vector system.

PubMed

Yoon, Hyerim; Song, Jin Myung; Ryu, Chun Jeih; Kim, Yeon-Gu; Lee, Eun Kyo; Kang, Sunghyun; Kim, Sang Jick

2012-09-18

Cell panning of phage-displayed antibody library is a powerful tool for the development of therapeutic and imaging agents since disease-related cell surface proteins in native complex conformation can be directly targeted. Here, we employed a strategy taking advantage of an integrated vector system which allows rapid conversion of scFv-displaying phage into scFv-Fc format for efficient cell-based scFv library selection on a tetraspanin protein, CD9. A mouse scFv library constructed by using a phagemid vector, pDR-D1 was subjected to cell panning against stable CD9 transfectant, and the scFv repertoire from the enriched phage pool was directly transferred to a mammalian cassette vector, pDR-OriP-Fc1. The resulting constructs enabled transient expression of enough amounts of scFv-Fcs in HEK293E cells, and flow cytometric screening of binders for CD9 transfectant could be performed simply by using the culture supernatants. All three clones selected from the screening showed correct CD9-specificity. They could immunoprecipitate CD9 molecules out of the transfectant cell lysate and correctly stain endogenous CD9 expression on cancer cell membrane. Furthermore, competition assay with a known anti-CD9 monoclonal antibody (mAb) suggested that the binding epitopes of some of them overlap with that of the mAb which resides within the large extracellular loop of CD9. This study demonstrates that scFv-Fc from mammalian transient expression can be chosen as a reliable format for rapid screening and validation in cell-based scFv library selection, and the strategy described here will be applicable to efficient discovery of antibodies to diverse cell-surface targets.

Numerical modeling of NO formation in laminar Bunsen flames -- A flamelet approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chou, C.P.; Chen, J.Y.; Yam, C.G.

1998-08-01

Based on the flamelet concept, a numerical model has been developed for fast predictions of NO{sub x} and CO emissions from laminar flames. The model is applied to studying NO formation in the secondary nonpremixed flame zone of fuel-rich methane Bunsen flames. By solving the steady-state flamelet equations with the detailed GR12.1 methane-air mechanism, a flamelet library is generated containing thermochemical information for a range of scalar dissipation rates at the ambient pressure condition. Modeling of NO formation is made by solving its conservation equation with chemical source term evaluated based on flamelet library using the extended Zeldovich mechanism andmore » NO reburning reactions. The optically-thin radiation heat transfer model is used to explore the potential effect of heat loss on thermal NO formation. The numerical scheme solves the two-dimensional Navier-Stokes equations as well as three additional equations: the mixture fraction, the NO mass fraction, and the enthalpy deficit due to radiative heat loss. With an established flamelet library, typical computing times are about 5 hours per calculation on a DEC-3000 300LX workstation. The predicted mixing field, radial temperature profiles, and NO distributions compare favorably with recent experimental data obtained by Nguyen et al. The dependence of NO{sub x} emission on equivalence ratio is studied numerically and the predictions are found to agree reasonably well with the measurements by Muss. The computed results show a decreasing trend of NO{sub x} emission with the equivalence ratio but an increasing trend in the CO emission index. By examining this trade-off between NO{sub x} and CO, an optimal equivalence ratio of 1.4 is found to yield the lowest combined emission.« less

Arcus v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Englehardt, Robert; Steele, Andrew

Arcus, developed by Sandia National Laboratories, is a library for calculating, parsing, formatting, converting and comparing both IPv4 and IPv6 addresses and subnets. It accounts for 128-bit numbers on 32-bit platforms.

78 FR 60784 - Incorporation By Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-02

...-FOIA) reading rooms, have made the print publication of the Federal Register unnecessary. They also... online access to standards was in a read-only format because someone reading the material at the library...

Outreach to Scientists and Engineers at the Hanford Technical Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buxton, Karen A.

Staff at the Hanford Technical Library has developed a suite of programs designed to help busy researchers at the Pacific Northwest National Laboratory (PNNL) make better use of library products and services. Programs include formal training classes, one-on-one consultations, and targeted email messages announcing new materials to researchers in specific fields. A staple of outreach has been to teach classes to library clients covering research tools in their fields. These classes started out in the library classroom and then expanded to other venues around PNNL. Class surveys indicated that many researchers desired a practical approach to learning rather than themore » traditional lecture format. The library instituted “Library Learning Day” and hosted classes in the PNNL computer training room to provide lab employees with a hands-on learning experience. Classes are generally offered at noon and lab staff attends classes on their lunch hour. Many just do not have time to spend a full hour in training. Library staff added some experimental half-hour mini classes in campus buildings geared to the projects and interests of researchers there to see if this format was more appealing. As other programs have developed librarians are teaching fewer classes but average attendance figures has remained fairly stable from 2005-2007. In summer of 2004 the library began the Traveling Librarian program. Librarians call-on groups and individuals in 24 buildings on the Richland Washington campus. Five full-time and two part-time librarians are involved in the program. Librarians usually send out email announcements prior to visits and encourage scientists and engineers to make appointments for a brief 15 minute consultation in the researcher’s own office. During the meeting lab staff learn about products or product features that can help them work more productively. Librarians also make cold calls to staff that do not request a consultation and may not be making full use of the library. Scientists and engineers who require longer sessions can arrange half-hour training appointments in the researcher’s own office or at the library. Since the program was implemented staff made 165 visits to 1249 laboratory staff including some repeat consultation requests. New acquisitions lists are sent to individuals and groups that would be interested in recent journal, database, and books purchases. These lists are topic specific and targeted to groups and individuals with an interest in the field. For example newly acquired engineering resources are targeted at engineering groups. The new acquisitions list for engineering began mid year in 2005. An analysis of circulation statistics for engineering books in fiscal year 2005, 2006, and 2007 show that circulation increased each year with 2007 circulation nearly double that of 2005. This took place when overall circulation rose in FY06 but fell slightly in FY07. Outreach strategies tailored and individualized can be effective. Offering multiple outreach options offers researchers different ways to interact with library staff and services.« less

Development of High Throughput Process for Constructing 454 Titanium and Illumina Libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshpande, Shweta; Hack, Christopher; Tang, Eric

2010-05-28

We have developed two processes with the Biomek FX robot to construct 454 titanium and Illumina libraries in order to meet the increasing library demands. All modifications in the library construction steps were made to enable the adaptation of the entire processes to work with the 96-well plate format. The key modifications include the shearing of DNA with Covaris E210 and the enzymatic reaction cleaning and fragment size selection with SPRI beads and magnetic plate holders. The construction of 96 Titanium libraries takes about 8 hours from sheared DNA to ssDNA recovery. The processing of 96 Illumina libraries takes lessmore » time than that of the Titanium library process. Although both processes still require manual transfer of plates from robot to other work stations such as thermocyclers, these robotic processes represent about 12- to 24-folds increase of library capacity comparing to the manual processes. To enable the sequencing of many libraries in parallel, we have also developed sets of molecular barcodes for both library types. The requirements for the 454 library barcodes include 10 bases, 40-60percent GC, no consecutive same base, and no less than 3 bases difference between barcodes. We have used 96 of the resulted 270 barcodes to construct libraries and pool to test the ability of accurately assigning reads to the right samples. When allowing 1 base error occurred in the 10 base barcodes, we could assign 99.6percent of the total reads and 100percent of them were uniquely assigned. As for the Illumina barcodes, the requirements include 4 bases, balanced GC, and at least 2 bases difference between barcodes. We have begun to assess the ability to assign reads after pooling different number of libraries. We will discuss the progress and the challenges of these scale-up processes.« less

Fission yields data generation and benchmarks of decay heat estimation of a nuclear fuel

NASA Astrophysics Data System (ADS)

Gil, Choong-Sup; Kim, Do Heon; Yoo, Jae Kwon; Lee, Jounghwa

2017-09-01

Fission yields data with the ENDF-6 format of 235U, 239Pu, and several actinides dependent on incident neutron energies have been generated using the GEF code. In addition, fission yields data libraries of ORIGEN-S, -ARP modules in the SCALE code, have been generated with the new data. The decay heats by ORIGEN-S using the new fission yields data have been calculated and compared with the measured data for validation in this study. The fission yields data ORIGEN-S libraries based on ENDF/B-VII.1, JEFF-3.1.1, and JENDL/FPY-2011 have also been generated, and decay heats were calculated using the ORIGEN-S libraries for analyses and comparisons.

Seismo-Live: Training in Seismology with Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Krischer, Lion; Tape, Carl; Igel, Heiner

2016-04-01

Seismological training tends to occur within the isolation of a particular institution with a limited set of tools (codes, libraries) that are often not transferrable outside. Here, we propose to overcome these limitations with a community-driven library of Jupyter notebooks dedicated to training on any aspect of seismology for purposes of education and outreach, on-site or archived tutorials for codes, classroom instruction, and research. A Jupyter notebook (jupyter.org) is an open-source interactive computational environment that allows combining code execution, rich text, mathematics, and plotting. It can be considered a platform that supports reproducible research, as all inputs and outputs may be stored. Text, external graphics, equations can be handled using Markdown (incl. LaTeX) format. Jupyter notebooks are driven by standard web browsers, can be easily exchanged in text format, or converted to other documents (e.g. PDF, slide shows). They provide an ideal format for practical training in seismology. A pilot-platform was setup with a dedicated server such that the Jupyter notebooks can be run in any browser (PC, notepad, smartphone). We show the functionalities of the Seismo-Live platform with examples from computational seismology, seismic data access and processing using the ObsPy library, seismic inverse problems, and others. The current examples are all using the Python programming language but any free language can be used. Potentially, such community platforms could be integrated with the EPOS-IT infrastructure and extended to other fields of Earth sciences.

Production of a Human Antibody Library in the Phage-Display Vector pSEX81.

PubMed

Welschof, M; Little, M; Dörsam, H

1998-01-01

Human monoclonal antibodies (MAbs) are more suitable than MAbs of animal origin for clinical applications because of lower hypersensitivity reactions, less formation of circulating immune complexes and lower anti-immunoglobulin responses The classical production of human MAbs via the hybridoma technique or Epstein-Barr virus (EBV) transformation is limited by the instability of cell lines, low antibody production, and the problems of imununizing humans with certain antigens (1,2). A promising alternative 1s the production of human recombinant antibodies (3). Recombinant DNA technology has made it possible to clone human antibody genes in vectors and to generate antibody expression libraries (4-7). One approach has been to amplify and recombine the IgG repertoire of an "immunized" donor. This has been used to isolate several antibodies related to diseases (8,9). In order to obtain more universal antibody libraries the naive IgM repertoire of several "unimmunized" donors were pooled (10,12). The complexity of the combinatorial libraries has been further increased by creating the so-called "semisynthetic" antibody libraries (22-14).

Software reuse example and challenges at NSIDC

NASA Astrophysics Data System (ADS)

Billingsley, B. W.; Brodzik, M.; Collins, J. A.

2009-12-01

NSIDC has created a new data discovery and access system, Searchlight, to provide users with the data they want in the format they want. NSIDC Searchlight supports discovery and access to disparate data types with on-the-fly reprojection, regridding and reformatting. Architected to both reuse open source systems and be reused itself, Searchlight reuses GDAL and Proj4 for manipulating data and format conversions, the netCDF Java library for creating netCDF output, MapServer and OpenLayers for defining spatial criteria and the JTS Topology Suite (JTS) in conjunction with Hibernate Spatial for database interaction and rich OGC-compliant spatial objects. The application reuses popular Java and Java Script libraries including Struts 2, Spring, JPA (Hibernate), Sitemesh, JFreeChart, JQuery, DOJO and a PostGIS PostgreSQL database. Future reuse of Searchlight components is supported at varying architecture levels, ranging from the database and model components to web services. We present the tools, libraries and programs that Searchlight has reused. We describe the architecture of Searchlight and explain the strategies deployed for reusing existing software and how Searchlight is built for reuse. We will discuss NSIDC reuse of the Searchlight components to support rapid development of new data delivery systems.

Creating the New from the Old: Combinatorial Libraries Generation with Machine-Learning-Based Compound Structure Optimization.

PubMed

Podlewska, Sabina; Czarnecki, Wojciech M; Kafel, Rafał; Bojarski, Andrzej J

2017-02-27

The growing computational abilities of various tools that are applied in the broadly understood field of computer-aided drug design have led to the extreme popularity of virtual screening in the search for new biologically active compounds. Most often, the source of such molecules consists of commercially available compound databases, but they can also be searched for within the libraries of structures generated in silico from existing ligands. Various computational combinatorial approaches are based solely on the chemical structure of compounds, using different types of substitutions for new molecules formation. In this study, the starting point for combinatorial library generation was the fingerprint referring to the optimal substructural composition in terms of the activity toward a considered target, which was obtained using a machine learning-based optimization procedure. The systematic enumeration of all possible connections between preferred substructures resulted in the formation of target-focused libraries of new potential ligands. The compounds were initially assessed by machine learning methods using a hashed fingerprint to represent molecules; the distribution of their physicochemical properties was also investigated, as well as their synthetic accessibility. The examination of various fingerprints and machine learning algorithms indicated that the Klekota-Roth fingerprint and support vector machine were an optimal combination for such experiments. This study was performed for 8 protein targets, and the obtained compound sets and their characterization are publically available at http://skandal.if-pan.krakow.pl/comb_lib/ .

GBParsy: a GenBank flatfile parser library with high speed.

PubMed

Lee, Tae-Ho; Kim, Yeon-Ki; Nahm, Baek Hie

2008-07-25

GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory. We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5-100x faster than current parsers in benchmark tests. GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.

An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification

PubMed Central

Sotelo, Pablo H.; Collazo, Noberto; Zuñiga, Roberto; Gutiérrez-González, Matías; Catalán, Diego; Ribeiro, Carolina Hager; Aguillón, Juan Carlos; Molina, María Carmen

2012-01-01

Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles. PMID:22692130

Performance evaluation of phage-displayed synthetic human single-domain antibody libraries: A retrospective analysis.

PubMed

Henry, Kevin A; Tanha, Jamshid

2018-05-01

Fully human synthetic single-domain antibodies (sdAbs) are desirable therapeutic molecules but their development is a considerable challenge. Here, using a retrospective analysis of in-house historical data, we examined the parameters that impact the outcome of screening phage-displayed synthetic human sdAb libraries to discover antigen-specific binders. We found no evidence for a differential effect of domain type (V H or V L ), library randomization strategy, incorporation of a stabilizing disulfide linkage or sdAb display format (monovalent vs. multivalent) on the probability of obtaining any antigen-binding human sdAbs, instead finding that the success of library screens was primarily related to properties of target antigens, especially molecular mass. The solubility and binding affinity of sdAbs isolated from successful screens depended both on properties of the sdAb libraries (primarily domain type) and the target antigens. Taking attrition of sdAbs with major manufacturability concerns (aggregation; low expression) and sdAbs that do not recognize native cell-surface antigens as independent probabilities, we calculate the overall likelihood of obtaining ≥1 antigen-binding human sdAb from a single library-target screen as ~24%. Successful library-target screens should be expected to yield ~1.3 human sdAbs on average, each with average binding affinity of ~2 μM. Copyright © 2018 Elsevier B.V. All rights reserved.

A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG.

PubMed

Xiao, Xiaodong; Douthwaite, Julie A; Chen, Yan; Kemp, Ben; Kidd, Sara; Percival-Alwyn, Jennifer; Smith, Alison; Goode, Kate; Swerdlow, Bonnie; Lowe, David; Wu, Herren; Dall'Acqua, William F; Chowdhury, Partha S

Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.

Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience

PubMed Central

Rübel, Oliver; Dougherty, Max; Prabhat; Denes, Peter; Conant, David; Chang, Edward F.; Bouchard, Kristofer

2016-01-01

Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat. PMID:27867355

LipidMiner: A Software for Automated Identification and Quantification of Lipids from Multiple Liquid Chromatography-Mass Spectrometry Data Files

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Da; Zhang, Qibin; Gao, Xiaoli

2014-04-30

We have developed a tool for automated, high-throughput analysis of LC-MS/MS data files, which greatly simplifies LC-MS based lipidomics analysis. Our results showed that LipidMiner is accurate and comprehensive in identification and quantification of lipid molecular species. In addition, the workflow implemented in LipidMiner is not limited to identification and quantification of lipids. If a suitable metabolite library is implemented in the library matching module, LipidMiner could be reconfigured as a tool for general metabolomics data analysis. It is of note that LipidMiner currently is limited to singly charged ions, although it is adequate for the purpose of lipidomics sincemore » lipids are rarely multiply charged,[14] even for the polyphosphoinositides. LipidMiner also only processes file formats generated from mass spectrometers from Thermo, i.e. the .RAW format. In the future, we are planning to accommodate file formats generated by mass spectrometers from other predominant instrument vendors to make this tool more universal.« less

Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats

NASA Astrophysics Data System (ADS)

Ghiringhelli, Luca M.; Carbogno, Christian; Levchenko, Sergey; Mohamed, Fawzi; Huhs, Georg; Lüders, Martin; Oliveira, Micael; Scheffler, Matthias

2017-11-01

With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

An OpenEarth Framework (OEF) for Integrating and Visualizing Earth Science Data

NASA Astrophysics Data System (ADS)

Moreland, J. L.; Nadeau, D. R.; Baru, C.; Crosby, C. J.

2009-12-01

The integration of data is essential to make transformative progress in understanding the complex processes operating at the Earth’s surface and within its interior. While our current ability to collect massive amounts of data, develop structural models, and generate high-resolution dynamics models is well developed, our ability to quantitatively integrate these data and models into holistic interpretations of Earth systems is poorly developed. We lack the basic tools to realize a first-order goal in Earth science of developing integrated 4D models of Earth structure and processes using a complete range of available constraints, at a time when the research agenda of major efforts such as EarthScope demand such a capability. Among the challenges to 3D data integration are data that may be in different coordinate spaces, units, value ranges, file formats, and data structures. While several file format standards exist, they are infrequently or incorrectly used. Metadata is often missing, misleading, or relegated to README text files along side the data. This leaves much of the work to integrate data bogged down by simple data management tasks. The OpenEarth Framework (OEF) being developed by GEON addresses these data management difficulties. The software incorporates file format parsers, data interpretation heuristics, user interfaces to prompt for missing information, and visualization techniques to merge data into a common visual model. The OEF’s data access libraries parse formal and de facto standard file formats and map their data into a common data model. The software handles file format quirks, storage details, caching, local and remote file access, and web service protocol handling. Heuristics are used to determine coordinate spaces, units, and other key data features. Where multiple data structure, naming, and file organization conventions exist, those heuristics check for each convention’s use to find a high confidence interpretation of the data. When no convention or embedded data yields a suitable answer, the user is prompted to fill in the blanks. The OEF’s interaction libraries assist in the construction of user interfaces for data management. These libraries support data import, data prompting, data introspection, the management of the contents of a common data model, and the creation of derived data to support visualization. Finally, visualization libraries provide interactive visualization using an extended version of NASA WorldWind. The OEF viewer supports visualization of terrains, point clouds, 3D volumes, imagery, cutting planes, isosurfaces, and more. Data may be color coded, shaded, and displayed above, or below the terrain, and always registered into a common coordinate space. The OEF architecture is open and cross-platform software libraries are available separately for use with other software projects, while modules from other projects may be integrated into the OEF to extend its features. The OEF is currently being used to visualize data from EarthScope-related research in the Western US.

General Guidelines on Criteria for Adoption or Rejection of Evaluated Libraries and Data by the Nuclear Data Team

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neudecker, Denise; Conlin, Jeremy Lloyd; Gray, Mark Girard

This memo contains general guidelines on what documentation and tools need to be in place as well as format and data testing requirements such that evaluated nuclear data sets or entire libraries can be adopted by the nuclear data team. Additional requirements beyond this memo might apply for specific nuclear data observables. These guidelines were established based on discussions between J.L. Conlin, M.G. Gray, A.P. McCartney, D. Neudecker, D.K. Parsons and M.C. White.

Why use case studies rather than simulation-gaming techniques or library research?

NASA Technical Reports Server (NTRS)

Mcdonald, S. W.

1981-01-01

Method which present a student with a more challenging and true to life situation of needing to conduct research in a problem solving context--and not thinking about organization of format until research and thinking are complete are investigated. Simulation-gaming techniques which attempt to teach initiative and creativity that library research are used for this purpose. However, it is shown case studies provide the greatest opportunities to engage the students in problem solving situations in which they develop skills as researchers and writers.

The influence of antibody fragment format on phage display based affinity maturation of IgG

PubMed Central

Steinwand, Miriam; Droste, Patrick; Frenzel, Andrè; Hust, Michael; Dübel, Stefan; Schirrmann, Thomas

2014-01-01

Today, most approved therapeutic antibodies are provided as immunoglobulin G (IgG), whereas small recombinant antibody formats are required for in vitro antibody generation and engineering during drug development. Particularly, single chain (sc) antibody fragments like scFv or scFab are well suited for phage display and bacterial expression, but some have been found to lose affinity during conversion into IgG.   In this study, we compared the influence of the antibody format on affinity maturation of the CD30-specific scFv antibody fragment SH313-F9, with the overall objective being improvement of the IgG. The variable genes of SH313-F9 were randomly mutated and then cloned into libraries encoding different recombinant antibody formats, including scFv, Fab, scFabΔC, and FabΔC. All tested antibody formats except Fab allowed functional phage display of the parental antibody SH313-F9, and the corresponding mutated antibody gene libraries allowed isolation of candidates with enhanced CD30 binding. Moreover, scFv and scFabΔC antibody variants retained improved antigen binding after subcloning into the single gene encoded IgG-like formats scFv-Fc or scIgG, but lost affinity after conversion into IgGs. Only affinity maturation using the Fab-like FabΔC format, which does not contain the carboxy terminal cysteines, allowed successful selection of molecules with improved binding that was retained after conversion to IgG. Thus, affinity maturation of IgGs is dependent on the antibody format employed for selection and screening. In this study, only FabΔC resulted in the efficient selection of IgG candidates with higher affinity by combination of Fab-like conformation and improved phage display compared with Fab. PMID:24262918

Constraining the Star-Formation and Metal-Enrichment Histories of Galaxies with the Next Generation Spectral Library

NASA Astrophysics Data System (ADS)

Heap, Sara

2009-07-01

Hubble's Next Generation Spectral Library {NGSL} comprises intermediate-resolution {R 1000} STIS spectra of 378 stars having a wide range in metallicity and age. Unique features of the NGSL include its broad wavelength coverage {1,800-10,100 ?} and high-S/N, absolute spectrophotometry. When incorporated in modern stellar population synthesis codes, the NGSL should enable us to constrain simultaneously the star-formation history and metal-enrichment history of galaxies over a wide redshift interval {z= 0-2}. In AR10659, we laid the foundation for tracing the spectral evolution of galaxies by putting the NGSL in order. We now propose to derive the atmospheric and fundamental parameters of the program stars, generate integrated spectra of stellar populations of different metallicities and initial mass functions, and derive spectral diagnostics of the age, metalllicity and E{B-V} of stellar populations.

Desktop document delivery using portable document format (PDF) files and the Web.

PubMed Central

Shipman, J P; Gembala, W L; Reeder, J M; Zick, B A; Rainwater, M J

1998-01-01

Desktop access to electronic full-text literature was rated one of the most desirable services in a client survey conducted by the University of Washington Libraries. The University of Washington Health Sciences Libraries (UW HSL) conducted a ten-month pilot test from August 1996 to May 1997 to determine the feasibility of delivering electronic journal articles via the Internet to remote faculty. Articles were scanned into Adobe Acrobat Portable Document Format (PDF) files and delivered to individuals using Multipurpose Internet Mail Extensions (MIME) standard e-mail attachments and the Web. Participants retrieved scanned articles and used the Adobe Acrobat Reader software to view and print files. The pilot test required a special programming effort to automate the client notification and file deletion processes. Test participants were satisfied with the pilot test despite some technical difficulties. Desktop delivery is now offered as a routine delivery method from the UW HSL. PMID:9681165

Desktop document delivery using portable document format (PDF) files and the Web.

PubMed

Shipman, J P; Gembala, W L; Reeder, J M; Zick, B A; Rainwater, M J

1998-07-01

Desktop access to electronic full-text literature was rated one of the most desirable services in a client survey conducted by the University of Washington Libraries. The University of Washington Health Sciences Libraries (UW HSL) conducted a ten-month pilot test from August 1996 to May 1997 to determine the feasibility of delivering electronic journal articles via the Internet to remote faculty. Articles were scanned into Adobe Acrobat Portable Document Format (PDF) files and delivered to individuals using Multipurpose Internet Mail Extensions (MIME) standard e-mail attachments and the Web. Participants retrieved scanned articles and used the Adobe Acrobat Reader software to view and print files. The pilot test required a special programming effort to automate the client notification and file deletion processes. Test participants were satisfied with the pilot test despite some technical difficulties. Desktop delivery is now offered as a routine delivery method from the UW HSL.

Implementing DSpace at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Lowe, Greta

2007-01-01

This presentation looks at the implementation of the DSpace institutional repository system at the NASA Langley Technical Library. NASA Langley Technical Library implemented DSpace software as a replacement for the Langley Technical Report Server (LTRS). DSpace was also used to develop the Langley Technical Library Digital Repository (LTLDR). LTLDR contains archival copies of core technical reports in the aeronautics area dating back to the NACA era and other specialized collections relevant to the NASA Langley community. Extensive metadata crosswalks were created to facilitate moving data from various systems and formats to DSpace. The Dublin Core metadata screens were also customized. The OpenURL standard and Ex Libris Metalib are being used in this environment to assist our customers with either discovering full-text content or with initiating a request for the item.

Selection of stable scFv antibodies by phage display.

PubMed

Brockmann, Eeva-Christine

2012-01-01

ScFv fragments are popular recombinant antibody formats but often suffer from limited stability. Phage display is a powerful tool in antibody engineering and applicable also for stability selection. ScFv variants with improved stability can be selected from large randomly mutated phage displayed libraries with a specific antigen after the unstable variants have been inactivated by heat or GdmCl. Irreversible scFv denaturation, which is a prerequisite for efficient selection, is achieved by combining denaturation with reduction of the intradomain disulfide bonds. Repeated selection cycles of increasing stringency result in enrichment of stabilized scFv fragments. Procedures for constructing a randomly mutated scFv library by error-prone PCR and phage display selection for enrichment of stable scFv antibodies from the library are described here.

Curatr: a web application for creating, curating and sharing a mass spectral library.

PubMed

Palmer, Andrew; Phapale, Prasad; Fay, Dominik; Alexandrov, Theodore

2018-04-15

We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation spectra for multiple adducts. An intuitive interface helps users to select high quality spectra that are stored along with searchable molecular information, the providence of each standard and experimental metadata. Curatr supports exports to several standard formats for use with third party software or submission to repositories. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library http://curatr.mcf.embl.de. Source code and example data are at http://github.com/alexandrovteam/curatr/. palmer@embl.de. Supplementary data are available at Bioinformatics online.

Integrating the Learning of Mathematics and Science Using Interactive Teaching and Learning Strategies

NASA Astrophysics Data System (ADS)

Holmes, Mark H.

2006-10-01

To help students grasp the intimate connections that exist between mathematics and its applications in other disciplines a library of interactive learning modules was developed. This library covers the mathematical areas normally studied by undergraduate students and is used in science courses at all levels. Moreover, the library is designed not just to provide critical connections across disciplines but to also provide longitudinal subject reinforcement as students progress in their studies. In the process of developing the modules a complete editing and publishing system was constructed that is optimized for automated maintenance and upgradeability of materials. The result is a single integrated production system for web-based educational materials. Included in this is a rigorous assessment program, involving both internal and external evaluations of each module. As will be seen, the formative evaluation obtained during the development of the library resulted in the modules successfully bridging multiple disciplines and breaking down the disciplinary barriers commonly found in their math and non-math courses.

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

PubMed Central

Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

2008-01-01

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

Buckets, Clusters and Dienst

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

1997-01-01

In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

The Hierarchical Data Format as a Foundation for Community Data Sharing

NASA Astrophysics Data System (ADS)

Habermann, T.

2017-12-01

Hierarchical Data Format (HDF) formats and libraries have been used by individual researchers and major science programs across many Earth and Space Science disciplines and sectors to provide high-performance information storage and access for several decades. Generic group, dataset, and attribute objects in HDF have been combined in many ways to form domain objects that scientists understand and use. Well-known applications of HDF in the Earth Sciences include thousands of global satellite observations and products produced by NASA's Earth Observing System using the HDF-EOS conventions, navigation quality bathymetry produced as Bathymetric Attributed Grids (BAGs) by the OpenNavigationSurface project and others, seismic wave collections written into the Adoptable Seismic Data Format (ASDF) and many oceanographic and atmospheric products produced using the climate-forecast conventions with the netCDF4 data model and API to HDF5. This is the modus operandi of these communities: 1) develop a model of scientific data objects and associated metadata used in a domain, 2) implement that model using HDF, 3) develop software libraries that connect that model to tools and 4) encourage adoption of those tools in the community. Understanding these domain object implementations and facilitating communication across communities is an important goal of The HDF Group. We will discuss these examples and approaches to community outreach during this session.

The mining of pearl formation genes in pearl oyster Pinctada fucata by cDNA suppression subtractive hybridization.

PubMed

Wang, Ning; Kinoshita, Shigeharu; Nomura, Naoko; Riho, Chihiro; Maeyama, Kaoru; Nagai, Kiyohito; Watabe, Shugo

2012-04-01

Recent researches revealed the regional preference of biomineralization gene transcription in the pearl oyster Pinctada fucata: it transcribed mainly the genes responsible for nacre secretion in mantle pallial, whereas the ones regulating calcite shells expressed in mantle edge. This study took use of this character and constructed the forward and reverse suppression subtractive hybridization (SSH) cDNA libraries. A total of 669 cDNA clones were sequenced and 360 expressed sequence tags (ESTs) greater than 100 bp were generated. Functional annotation associated 95 ESTs with specific functions, and 79 among them were identified from P. fucata at the first time. In the forward SSH cDNA library, it recognized mass amount of nacre protein genes, biomineralization genes dominantly expressed in the mantle pallial, calcium-ion-binding genes, and other biomineralization-related genes important for pearl formation. Real-time PCR showed that all the examined genes were distributed in oyster mantle tissues with a consistence to the SSH design. The detection of their RNA transcripts in pearl sac confirmed that the identified genes were certainly involved in pearl formation. Therefore, the data from this work will initiate a new round of pearl formation gene study and shed new insights into molluscan biomineralization.

Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep).

PubMed

Guellouz, Asma; Valerio-Lepiniec, Marie; Urvoas, Agathe; Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.

Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep)

PubMed Central

Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a “filtration” procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×109 independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties. PMID:24014183

ARCGRAPH SYSTEM - AMES RESEARCH GRAPHICS SYSTEM

NASA Technical Reports Server (NTRS)

Hibbard, E. A.

1994-01-01

Ames Research Graphics System, ARCGRAPH, is a collection of libraries and utilities which assist researchers in generating, manipulating, and visualizing graphical data. In addition, ARCGRAPH defines a metafile format that contains device independent graphical data. This file format is used with various computer graphics manipulation and animation packages at Ames, including SURF (COSMIC Program ARC-12381) and GAS (COSMIC Program ARC-12379). In its full configuration, the ARCGRAPH system consists of a two stage pipeline which may be used to output graphical primitives. Stage one is associated with the graphical primitives (i.e. moves, draws, color, etc.) along with the creation and manipulation of the metafiles. Five distinct data filters make up stage one. They are: 1) PLO which handles all 2D vector primitives, 2) POL which handles all 3D polygonal primitives, 3) RAS which handles all 2D raster primitives, 4) VEC which handles all 3D raster primitives, and 5) PO2 which handles all 2D polygonal primitives. Stage two is associated with the process of displaying graphical primitives on a device. To generate the various graphical primitives, create and reprocess ARCGRAPH metafiles, and access the device drivers in the VDI (Video Device Interface) library, users link their applications to ARCGRAPH's GRAFIX library routines. Both FORTRAN and C language versions of the GRAFIX and VDI libraries exist for enhanced portability within these respective programming environments. The ARCGRAPH libraries were developed on a VAX running VMS. Minor documented modification of various routines, however, allows the system to run on the following computers: Cray X-MP running COS (no C version); Cray 2 running UNICOS; DEC VAX running BSD 4.3 UNIX, or Ultrix; SGI IRIS Turbo running GL2-W3.5 and GL2-W3.6; Convex C1 running UNIX; Amhdahl 5840 running UTS; Alliant FX8 running UNIX; Sun 3/160 running UNIX (no native device driver); Stellar GS1000 running Stellex (no native device driver); and an SGI IRIS 4D running IRIX (no native device driver). Currently with version 7.0 of ARCGRAPH, the VDI library supports the following output devices: A VT100 terminal with a RETRO-GRAPHICS board installed, a VT240 using the Tektronix 4010 emulation capability, an SGI IRIS turbo using the native GL2 library, a Tektronix 4010, a Tektronix 4105, and the Tektronix 4014. ARCGRAPH version 7.0 was developed in 1988.

From the ORFeome concept to highly comprehensive, full-genome screening libraries.

PubMed

Rid, Raphaela; Abdel-Hadi, Omar; Maier, Richard; Wagner, Martin; Hundsberger, Harald; Hintner, Helmut; Bauer, Johann; Onder, Kamil

2013-02-01

Recombination-based cloning techniques have in recent times facilitated the establishment of genome-scale single-gene ORFeome repositories. Their further handling and downstream application in systematic fashion is, however, practically impeded because of logistical plus economic challenges. At this juncture, simultaneously transferring entire gene collections in compiled pool format could represent an advanced compromise between systematic ORFeome (an organism's entire set of protein-encoding open reading frames) projects and traditional random library approaches, but has not yet been considered in great detail. In our endeavor to merge the comprehensiveness of ORFeomes with a basically simple, streamlined, and easily executable single-tube design, we have here produced five different pooled screening-ready libraries for both Staphylococcus aureus and Homo sapiens. By evaluating the parallel transfer efficiencies of differentially sized genes from initial polymerase chain reaction (PCR) product amplification to entry and final destination library construction via quantitative real-time PCR, we found that the complexity of the gene population is fairly stably maintained once an entry resource has been successfully established, and that no apparent size-selection bias loss of large inserts takes place. Recombinational transfer processes are hence robust enough for straightforwardly achieving such pooled screening libraries.

Identification of Osteoconductive and Biodegradable Polymers from a Combinatorial Polymer Library

PubMed Central

Brey, Darren M.; Chung, Cindy; Hankenson, Kurt D.; Garino, Jonathon P.; Burdick, Jason A.

2012-01-01

Combinatorial polymer syntheses are now being utilized to create libraries of materials with potential utility for a wide variety of biomedical applications. We recently developed a library of photopolymerizable and biodegradable poly(β-amino ester)s (PBAEs) that possessed a range of tunable properties. In this work, the PBAE library was assessed for candidate materials that met design criteria (e.g., physical properties such as degradation and mechanical strength and in vitro cell viability and osteoconductive behavior) for scaffolding in mineralized tissue repair. The most promising candidate, A6, was then processed into 3-dimensional porous scaffolds and implanted subcutaneously and only presented a mild inflammatory response. The scaffolds were then implanted intramuscularly and into a critically-sized cranial defect either alone or loaded with bone morphogenetic protein-2 (BMP-2). The samples in both locations displayed mineralized tissue formation in the presence of BMP-2, as evident through radiographs, micro-computed tomography, and histology, while samples without BMP-2 showed minimal or no mineralized tissue. These results illustrate a process to identify a candidate scaffolding material from a combinatorial polymer library, and specifically for the identification of an osteoconductive scaffold with osteoinductive properties via the inclusion of a growth factor. PMID:20198696

The comparative importance of books: clinical psychology in the health sciences library.

PubMed Central

Wehmeyer, J M; Wehmeyer, S

1999-01-01

Clinical psychology has received little attention as a subject in health sciences library collections. This study seeks to demonstrate the relative importance of the monographic literature to clinical psychology through the examination of citations in graduate student theses and dissertations at the Fordham Health Sciences Library, Wright State University. Dissertations and theses were sampled randomly; citations were classified by format, counted, and subjected to statistical analysis. Books and book chapters together account for 35% of the citations in clinical psychology dissertations, 25% in nursing theses, and 8% in biomedical sciences theses and dissertations. Analysis of variance indicates that the citations in dissertations and theses in the three areas differ significantly (F = 162.2 with 2 and 253 degrees of freedom, P = 0.0001). Dissertations and theses in biomedical sciences and nursing theses both cite significantly more journals per book than the dissertations in clinical psychology. These results support the hypothesis that users of clinical psychology literature rely more heavily on books than many other users of a health sciences library. Problems with using citation analyses in a single subject to determine a serials to monographs ratio for a health sciences library are pointed out. PMID:10219478

Entrepreneurial Spirit in Strategic Planning.

ERIC Educational Resources Information Center

Riggs, Donald E.

1987-01-01

Presents a model which merges the concepts of entrepreneurship with those of strategic planning to create a library management system. Each step of the process, including needs assessment and policy formation, strategy choice and implementation, and evaluation, is described in detail. (CLB)

Systematic reviews and meta-analyses on treatment of asthma: critical evaluation

PubMed Central

Jadad, Alejandro R; Moher, Michael; Browman, George P; Booker, Lynda; Sigouin, Christopher; Fuentes, Mario; Stevens, Robert

2000-01-01

Objective To evaluate the clinical, methodological, and reporting aspects of systematic reviews and meta-analyses on the treatment of asthma and to compare those published by the Cochrane Collaboration with those published in paper based journals. Design Analysis of studies identified from Medline, CINAHL, HealthSTAR, EMBASE, Cochrane Library, personal collections, and reference lists. Studies Articles describing a systematic review or a meta-analysis of the treatment of asthma that were published as a full report, in any language or format, in a peer reviewed journal or the Cochrane Library. Main outcome measures General characteristics of studies reviewed and methodological characteristics (sources of articles; language restrictions; format, design, and publication status of studies included; type of data synthesis; and methodological quality). Results 50 systematic reviews and meta-analyses were included. More than half were published in the past two years. Twelve reviews were published in the Cochrane Library and 38 were published in 22 peer reviewed journals. Forced expiratory volume in one second was the most frequently used outcome, but few reviews evaluated the effect of treatment on costs or patient preferences. Forty reviews were judged to have serious or extensive flaws. All six reviews associated with industry were in this group. Seven of the 10 most rigorous reviews were published in the Cochrane Library. Conclusions Most reviews published in peer reviewed journals or funded by industry have serious methodological flaws that limit their value to guide decisions. Cochrane reviews are more rigorous and better reported than those published in peer reviewed journals. PMID:10688558

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions.

PubMed

Weimar, M R; Cheung, J; Dey, D; McSweeney, C; Morrison, M; Kobayashi, Y; Whitman, W B; Carbone, V; Schofield, L R; Ronimus, R S; Cook, G M

2017-08-01

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H 2 and CO 2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions. IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions. Copyright © 2017 American Society for Microbiology.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

PubMed Central

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow. PMID:25565494

Building the interspace: Digital library infrastructure for a University Engineering Community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schatz, B.

A large-scale digital library is being constructed and evaluated at the University of Illinois, with the goal of bringing professional search and display to Internet information services. A testbed planned to grow to 10K documents and 100K users is being constructed in the Grainger Engineering Library Information Center, as a joint effort of the University Library and the National Center for Supercomputing Applications (NCSA), with evaluation and research by the Graduate School of Library and Information Science and the Department of Computer Science. The electronic collection will be articles from engineering and science journals and magazines, obtained directly from publishersmore » in SGML format and displayed containing all text, figures, tables, and equations. The publisher partners include IEEE Computer Society, AIAA (Aerospace Engineering), American Physical Society, and Wiley & Sons. The software will be based upon NCSA Mosaic as a network engine connected to commercial SGML displayers and full-text searchers. The users will include faculty/students across the midwestern universities in the Big Ten, with evaluations via interviews, surveys, and transaction logs. Concurrently, research into scaling the testbed is being conducted. This includes efforts in computer science, information science, library science, and information systems. These efforts will evaluate different semantic retrieval technologies, including automatic thesaurus and subject classification graphs. New architectures will be designed and implemented for a next generation digital library infrastructure, the Interspace, which supports interaction with information spread across information spaces within the Net.« less

BASIC: A Simple and Accurate Modular DNA Assembly Method.

PubMed

Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

2017-01-01

Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae

PubMed Central

2017-01-01

Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle’s high O2 consumption and the presence of bacterial-type iron–sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae in which transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome. Two combinatorial libraries of nif gene clusters were constructed: a library of mitochondrial leading sequences consisting of 24 clusters within four subsets of nif gene expression strength, and an expression library of 72 clusters with fixed mitochondrial leading sequences and nif expression levels assigned according to factorial design. In total, 29 promoters and 18 terminators were combined to adjust nif gene expression levels. Expression and mitochondrial targeting was confirmed at the protein level as immunoblot analysis showed that Nif proteins could be efficiently accumulated in mitochondria. NifDK tetramer formation, an essential step of nitrogenase assembly, was experimentally proven both in cell-free extracts and in purified NifDK preparations. This work represents a first step toward obtaining functional nitrogenase in the mitochondria of a eukaryotic cell. PMID:28221768

SSL - THE SIMPLE SOCKETS LIBRARY

NASA Technical Reports Server (NTRS)

Campbell, C. E.

1994-01-01

The Simple Sockets Library (SSL) allows C programmers to develop systems of cooperating programs using Berkeley streaming Sockets running under the TCP/IP protocol over Ethernet. The SSL provides a simple way to move information between programs running on the same or different machines and does so with little overhead. The SSL can create three types of Sockets: namely a server, a client, and an accept Socket. The SSL's Sockets are designed to be used in a fashion reminiscent of the use of FILE pointers so that a C programmer who is familiar with reading and writing files will immediately feel comfortable with reading and writing with Sockets. The SSL consists of three parts: the library, PortMaster, and utilities. The user of the SSL accesses it by linking programs to the SSL library. The PortMaster initializes connections between clients and servers. The PortMaster also supports a "firewall" facility to keep out socket requests from unapproved machines. The "firewall" is a file which contains Internet addresses for all approved machines. There are three utilities provided with the SSL. SKTDBG can be used to debug programs that make use of the SSL. SPMTABLE lists the servers and port numbers on requested machine(s). SRMSRVR tells the PortMaster to forcibly remove a server name from its list. The package also includes two example programs: multiskt.c, which makes multiple accepts on one server, and sktpoll.c, which repeatedly attempts to connect a client to some server at one second intervals. SSL is a machine independent library written in the C-language for computers connected via Ethernet using the TCP/IP protocol. It has been successfully compiled and implemented on a variety of platforms, including Sun series computers running SunOS, DEC VAX series computers running VMS, SGI computers running IRIX, DECstations running ULTRIX, DEC alpha AXPs running OSF/1, IBM RS/6000 computers running AIX, IBM PC and compatibles running BSD/386 UNIX and HP Apollo 3000/4000/9000/400T computers running HP-UX. SSL requires 45K of RAM to run under SunOS and 80K of RAM to run under VMS. For use on IBM PC series computers and compatibles running DOS, SSL requires Microsoft C 6.0 and the Wollongong TCP/IP package. Source code for sample programs and debugging tools are provided. The documentation is available on the distribution medium in TeX and PostScript formats. The standard distribution medium for SSL is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format and a 5.25 inch 360K MS-DOS format diskette. The SSL was developed in 1992 and was updated in 1993.

ASDF: An Adaptable Seismic Data Format with Full Provenance

NASA Astrophysics Data System (ADS)

Smith, J. A.; Krischer, L.; Tromp, J.; Lefebvre, M. P.

2015-12-01

In order for seismologists to maximize their knowledge of how the Earth works, they must extract the maximum amount of useful information from all recorded seismic data available for their research. This requires assimilating large sets of waveform data, keeping track of vast amounts of metadata, using validated standards for quality control, and automating the workflow in a careful and efficient manner. In addition, there is a growing gap between CPU/GPU speeds and disk access speeds that leads to an I/O bottleneck in seismic workflows. This is made even worse by existing seismic data formats that were not designed for performance and are limited to a few fixed headers for storing metadata.The Adaptable Seismic Data Format (ASDF) is a new data format for seismology that solves the problems with existing seismic data formats and integrates full provenance into the definition. ASDF is a self-describing format that features parallel I/O using the parallel HDF5 library. This makes it a great choice for use on HPC clusters. The format integrates the standards QuakeML for seismic sources and StationXML for receivers. ASDF is suitable for storing earthquake data sets, where all waveforms for a single earthquake are stored in a one file, ambient noise cross-correlations, and adjoint sources. The format comes with a user-friendly Python reader and writer that gives seismologists access to a full set of Python tools for seismology. There is also a faster C/Fortran library for integrating ASDF into performance-focused numerical wave solvers, such as SPECFEM3D_GLOBE. Finally, a GUI tool designed for visually exploring the format exists that provides a flexible interface for both research and educational applications. ASDF is a new seismic data format that offers seismologists high-performance parallel processing, organized and validated contents, and full provenance tracking for automated seismological workflows.

Command Center Library Model Document. Comprehensive Approach to Reusable Defense Software (CARDS)

DTIC Science & Technology

1992-05-31

system, and functionality for specifying the layout of the document. 3.7.16.1 FrameMaker FrameMaker is a Commercial Off The Shelf (COTS) component...facilitating WYSIWYG creation of formatted reports with embedded graphics. FrameMaker is an advanced publishing tool that integrates word processing...available for the component FrameMaker : * Product evaluation reports in ASCII and postscript formats • Product assessment on line in model 0 Product

LONGLIB - A GRAPHICS LIBRARY

NASA Technical Reports Server (NTRS)

Long, D.

1994-01-01

This library is a set of subroutines designed for vector plotting to CRT's, plotters, dot matrix, and laser printers. LONGLIB subroutines are invoked by program calls similar to standard CALCOMP routines. In addition to the basic plotting routines, LONGLIB contains an extensive set of routines to allow viewport clipping, extended character sets, graphic input, shading, polar plots, and 3-D plotting with or without hidden line removal. LONGLIB capabilities include surface plots, contours, histograms, logarithm axes, world maps, and seismic plots. LONGLIB includes master subroutines, which are self-contained series of commonly used individual subroutines. When invoked, the master routine will initialize the plotting package, and will plot multiple curves, scatter plots, log plots, 3-D plots, etc. and then close the plot package, all with a single call. Supported devices include VT100 equipped with Selanar GR100 or GR100+ boards, VT125s, VT240s, VT220 equipped with Selanar SG220, Tektronix 4010/4014 or 4107/4109 and compatibles, and Graphon GO-235 terminals. Dot matrix printer output is available by using the provided raster scan conversion routines for DEC LA50, Printronix printers, and high or low resolution Trilog printers. Other output devices include QMS laser printers, Postscript compatible laser printers, and HPGL compatible plotters. The LONGLIB package includes the graphics library source code, an on-line help library, scan converter and meta file conversion programs, and command files for installing, creating, and testing the library. The latest version, 5.0, is significantly enhanced and has been made more portable. Also, the new version's meta file format has been changed and is incompatible with previous versions. A conversion utility is included to port the old meta files to the new format. Color terminal plotting has been incorporated. LONGLIB is written in FORTRAN 77 for batch or interactive execution and has been implemented on a DEC VAX series computer operating under VMS. This program was developed in 1985, and last updated in 1988.

Preparing for ENDF/B-VIII

NASA Astrophysics Data System (ADS)

Brown, David

2017-09-01

Although the next major release of the ENDF/B library is not due until the 2017-2018 time frame, ENDF/B-VIII is already positioned to become the most important release of the library in some time. ENDF/B-VIII will be built around the Neutron Reaction Standards as well as the 1H, 16O, 56Fe, 235U, 238U and 239Pu evaluations developed as part of the Coordinated International Evaluation Library Organization (CIELO) pilot project. In this contribution, we summarize these improvements as well as the many other improvements to ENDF that have already been made or are scheduled to be made in the next year. Improvements already included in the ENDF/B-VIII beta releases: • Aggressive use of the flexible and physically correct LRF=7 resolved resonance format in 12 updated evaluations (35,37Cl, 40Ca, 54,56,57Fe, 63,65Cu and 182,183,184,186W) • Thermal capture gammas from the EGAF project (6,7Li, 11B, 19F, 23Na, 27Al, 28Si, 35,37Cl) • Thermal Scattering Law evaluations from NCSU (α and β phase SiO2, SiC, lucite, BeO, and polyethylene) and from the CAB-CNL collaboration (heavy and light water) • Many new evaluations in the neutron sublibrary (n, 12,13C, 40Ar, 54,57,58Fe, 58,59,60,61,62,64Ni, 63,65Cu, 73As, 120Sn, 236m1Np) Inclusion of Red Cullen's EPICS2014 library, updating the photo-atomic, electron and atomic-relaxation sublibraries. Many improvements are planned in the next year including new evaluations such as charged particle evaluations translated from LLNL's ECPL. In addition to these major changes, ENDF/B-VIII will be the first official library released simultaneously in the legacy ENDF-6 and the newly developed Generalized Nuclear Data (GND) formats.

Climatic context and ecological implications of summer fog decline in the coast redwood region

PubMed Central

Johnstone, James A.; Dawson, Todd E.

2010-01-01

Biogeographical, physiological, and paleoecological evidence suggests that the coast redwood [Sequoia sempervirens (D. Don) Endl.] is closely associated with the presence of summer marine fog along the Pacific coast of California. Here we present a novel record of summer fog frequency in the coast redwood region upon the basis of direct hourly measurements of cloud ceiling heights from 1951 to 2008. Our analysis shows that coastal summer fog frequency is a remarkably integrative measure of United States Pacific coastal climate, with strong statistical connections to the wind-driven upwelling system of the California Current and the broad ocean temperature pattern known as the Pacific Decadal Oscillation. By using a long-term index of daily maximum land temperatures, we infer a 33% reduction in fog frequency since the early 20th century. We present tree physiological data suggesting that coast redwood and other ecosystems along the United States west coast may be increasingly drought stressed under a summer climate of reduced fog frequency and greater evaporative demand. PMID:20160112

Climatic context and ecological implications of summer fog decline in the coast redwood region.

PubMed

Johnstone, James A; Dawson, Todd E

2010-03-09

Biogeographical, physiological, and paleoecological evidence suggests that the coast redwood [Sequoia sempervirens (D. Don) Endl.] is closely associated with the presence of summer marine fog along the Pacific coast of California. Here we present a novel record of summer fog frequency in the coast redwood region upon the basis of direct hourly measurements of cloud ceiling heights from 1951 to 2008. Our analysis shows that coastal summer fog frequency is a remarkably integrative measure of United States Pacific coastal climate, with strong statistical connections to the wind-driven upwelling system of the California Current and the broad ocean temperature pattern known as the Pacific Decadal Oscillation. By using a long-term index of daily maximum land temperatures, we infer a 33% reduction in fog frequency since the early 20th century. We present tree physiological data suggesting that coast redwood and other ecosystems along the United States west coast may be increasingly drought stressed under a summer climate of reduced fog frequency and greater evaporative demand.

Advances in Synthetic Peptides Reagent Discovery

DTIC Science & Technology

2013-07-01

to promote specific and high affinity binding. Longer incubations may result in nonspecific attachment, such as early biofilm formation. Because...peptide libraries yields ligand arrays that classify breast tumor subtypes,” Molecular Cancer Therapeutics, 8(5), 1312-1318 (2009). [26] J. M. Kogot

National Cartographic Information Center Newsletter No. 8

USGS Publications Warehouse

,

1978-01-01

In this issue we cover several interesting topics, including a report on the NCIC/Special Libraries Association meeting in Denver, the launching of a third Landsat satellite with a new thermal band, and the formation of a new California map society.

Granting Each Equal Access.

ERIC Educational Resources Information Center

Walling, Linda Lucas

1992-01-01

Summarizes federal legislation regarding equal access for students with disabilities and discusses environmental barriers to accessibility in the library media center. Solutions to these design problems are suggested in the following areas: material formats and space requirements; the physical setting, including furniture, floor coverings,…

MISR Regional VBBE Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:   Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional UAE2 Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

Communicating with the Public: Getting It into Print.

ERIC Educational Resources Information Center

Dyal, Donald

1988-01-01

Discusses the advantages for libraries of utilizing print media for public information and public relations. News releases, interest stories, and feature stories are described, and hints on writing style for each format and on getting items printed are offered. (MES)

Comparison of bioluminescent kinase assays using substrate depletion and product formation.

PubMed

Tanega, Cordelle; Shen, Min; Mott, Bryan T; Thomas, Craig J; MacArthur, Ryan; Inglese, James; Auld, Douglas S

2009-12-01

Assays for ATPases have been enabled for high-throughput screening (HTS) by employing firefly luciferase to detect the remaining ATP in the assay. However, for any enzyme assay, measurement of product formation is a more sensitive assay design. Recently, technologies that allow detection of the ADP product from ATPase reactions have been described using fluorescent methods of detection. We describe here the characterization of a bioluminescent assay that employs firefly luciferase in a coupled-enzyme assay format to enable detection of ADP levels from ATPase assays (ADP-Glo, Promega Corp.). We determined the performance of the ADP-Glo assay in 1,536-well microtiter plates using the protein kinase Clk4 and a 1,352 member kinase focused combinatorial library. The ADP-Glo assay was compared to the Clk4 assay performed using a bioluminescence ATP-depletion format (Kinase-Glo, Promega Corp). We performed this analysis using quantitative HTS (qHTS) where we determined potency values for all library members and identified approximately 300 compounds with potencies ranging from as low as 50 nM to >10 microM, yielding a robust dataset for the comparison. Both assay formats showed high performance (Z'-factors approximately 0.9) and showed a similar potency distribution for the actives. We conclude that the bioluminescence ADP detection assay system is a viable generic alternative to the widely used ATP-depletion assay for ATPases and discuss the advantages and disadvantages of both approaches.

GRACKLE: a chemistry and cooling library for astrophysics

NASA Astrophysics Data System (ADS)

Smith, Britton D.; Bryan, Greg L.; Glover, Simon C. O.; Goldbaum, Nathan J.; Turk, Matthew J.; Regan, John; Wise, John H.; Schive, Hsi-Yu; Abel, Tom; Emerick, Andrew; O'Shea, Brian W.; Anninos, Peter; Hummels, Cameron B.; Khochfar, Sadegh

2017-04-01

We present the GRACKLE chemistry and cooling library for astrophysical simulations and models. GRACKLE provides a treatment of non-equilibrium primordial chemistry and cooling for H, D and He species, including H2 formation on dust grains; tabulated primordial and metal cooling; multiple ultraviolet background models; and support for radiation transfer and arbitrary heat sources. The library has an easily implementable interface for simulation codes written in C, C++ and FORTRAN as well as a PYTHON interface with added convenience functions for semi-analytical models. As an open-source project, GRACKLE provides a community resource for accessing and disseminating astrochemical data and numerical methods. We present the full details of the core functionality, the simulation and PYTHON interfaces, testing infrastructure, performance and range of applicability. GRACKLE is a fully open-source project and new contributions are welcome.

Arrayed antibody library technology for therapeutic biologic discovery.

PubMed

Bentley, Cornelia A; Bazirgan, Omar A; Graziano, James J; Holmes, Evan M; Smider, Vaughn V

2013-03-15

Traditional immunization and display antibody discovery methods rely on competitive selection amongst a pool of antibodies to identify a lead. While this approach has led to many successful therapeutic antibodies, targets have been limited to proteins which are easily purified. In addition, selection driven discovery has produced a narrow range of antibody functionalities focused on high affinity antagonism. We review the current progress in developing arrayed protein libraries for screening-based, rather than selection-based, discovery. These single molecule per microtiter well libraries have been screened in multiplex formats against both purified antigens and directly against targets expressed on the cell surface. This facilitates the discovery of antibodies against therapeutically interesting targets (GPCRs, ion channels, and other multispanning membrane proteins) and epitopes that have been considered poorly accessible to conventional discovery methods. Copyright © 2013. Published by Elsevier Inc.

A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster.

PubMed

White, K Makay; Matthews, Melinda K; Hughes, Rachel C; Sommer, Andrew J; Griffitts, Joel S; Newell, Peter D; Chaston, John M

2018-03-28

A metagenome wide association (MGWA) study of bacterial host association determinants in Drosophila predicted that LPS biosynthesis genes are significantly associated with host colonization. We were unable to create site-directed mutants for each of the predicted genes in Acetobacter , so we created an arrayed transposon insertion library using Acetobacter fabarum DsW_054 isolated from Drosophila Creation of the A. fabarum DsW_054 gene knock-out library was performed by combinatorial mapping and Illumina sequencing of random transposon insertion mutants. Transposon insertion locations for 6,418 mutants were successfully mapped, including hits within 63% of annotated genes in the A. fabarum DsW_054 genome. For 45/45 members of the library, insertion sites were verified by arbitrary PCR and Sanger sequencing. Mutants with insertions in four different LPS biosynthesis genes were selected from the library to validate the MGWA predictions. Insertion mutations in two genes biosynthetically upstream of Lipid-A formation, lpxC and lpxB , show significant differences in host association, whereas mutations in two genes encoding LPS biosynthesis functions downstream of Lipid-A biosynthesis had no effect. These results suggest an impact of bacterial cell surface molecules on the bacterial capacity for host association. Also, the transposon insertion mutant library will be a useful resource for ongoing research on the genetic basis for Acetobacter traits. Copyright © 2018 White et al.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

PubMed

Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

2016-01-01

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand Optimization

PubMed Central

Liu, Fa; Stephen, Andrew G.; Waheed, Abdul A.; Aman, M. Javad; Freed, Eric O.; Fisher, Robert J.; Burke, Terrence R.

2008-01-01

HIV-1 viral assembly requires a direct interaction between a Pro-Thr-Ala-Pro (“PTAP”) motif in the viral protein Gag-p6 and the cellular endosomal sorting factor Tsg101. In an effort to develop competitive inhibitors of this interaction, an SAR study was conducted based on the application of post solid-phase oxime formation involving the sequential insertion of aminooxy-containing residues within a nonamer parent peptide followed by reaction with libraries of aldehydes. Approximately 15–20-fold enhancement in binding affinity was achieved by this approach. PMID:18655064

An Electron/Photon/Relaxation Data Library for MCNP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, III, H. Grady

The capabilities of the MCNP6 Monte Carlo code in simulation of electron transport, photon transport, and atomic relaxation have recently been significantly expanded. The enhancements include not only the extension of existing data and methods to lower energies, but also the introduction of new categories of data and methods. Support of these new capabilities has required major additions to and redesign of the associated data tables. In this paper we present the first complete documentation of the contents and format of the new electron-photon-relaxation data library now available with the initial production release of MCNP6.

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

PubMed

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Embedding and Publishing Interactive, 3-Dimensional, Scientific Figures in Portable Document Format (PDF) Files

PubMed Central

Barnes, David G.; Vidiassov, Michail; Ruthensteiner, Bernhard; Fluke, Christopher J.; Quayle, Michelle R.; McHenry, Colin R.

2013-01-01

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2). PMID:24086243

Embedding and publishing interactive, 3-dimensional, scientific figures in Portable Document Format (PDF) files.

PubMed

Barnes, David G; Vidiassov, Michail; Ruthensteiner, Bernhard; Fluke, Christopher J; Quayle, Michelle R; McHenry, Colin R

2013-01-01

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2).

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

PubMed Central

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/ PMID:21713110

HDF4 Maps: For Now and For the Future

NASA Astrophysics Data System (ADS)

Plutchak, J.; Aydt, R.; Folk, M. J.

2013-12-01

Data formats and access tools necessarily change as technology improves to address emerging requirements with new capabilities. This on-going process inevitably leaves behind significant data collections in legacy formats that are difficult to support and sustain. NASA ESDIS and The HDF Group currently face this problem with large and growing archives of data in HDF4, an older version of the HDF format. Indefinitely guaranteeing the ability to read these data with multi-platform libraries in many languages is very difficult. As an alternative, HDF and NASA worked together to create maps of the files that contain metadata and information about data types, locations, and sizes of data objects in the files. These maps are written in XML and have successfully been used to access and understand data in HDF4 files without the HDF libraries. While originally developed to support sustainable access to these data, these maps can also be used to provide access to HDF4 metadata, facilitate user understanding of files prior to download, and validate the files for compliance with particular conventions. These capabilities are now available as a service for HDF4 archives and users.

A standard format and a graphical user interface for spin system specification.

PubMed

Biternas, A G; Charnock, G T P; Kuprov, Ilya

2014-03-01

We introduce a simple and general XML format for spin system description that is the result of extensive consultations within Magnetic Resonance community and unifies under one roof all major existing spin interaction specification conventions. The format is human-readable, easy to edit and easy to parse using standard XML libraries. We also describe a graphical user interface that was designed to facilitate construction and visualization of complicated spin systems. The interface is capable of generating input files for several popular spin dynamics simulation packages. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

MARC and Relational Databases.

ERIC Educational Resources Information Center

Llorens, Jose; Trenor, Asuncion

1993-01-01

Discusses the use of MARC format in relational databases and addresses problems of incompatibilities. A solution is presented that is in accordance with Open Systems Interconnection (OSI) standards and is based on experiences at the library of the Universidad Politecnica de Valencia (Spain). (four references) (EA)

Clio's Workshop: Resources for Historical Studies in American Librarianship.

ERIC Educational Resources Information Center

Tucker, John Mark

2000-01-01

Identifies tools most useful in the library historian's workshop, particularly those of a bibliographic, reference, or documentary nature. Highlights include bibliographic tools and the formative years of librarianship; sources of current scholarship; reference sources, including minority voices; documentary materials; and historians in…

The GPO Reduced to Size: Microforms and Government Publications.

ERIC Educational Resources Information Center

Zink, Steven D.

1983-01-01

Identifies format-specific problems which depository and other government publications librarians frequently face as a result of the Government Printing Office's (GPO) micropublishing program. Program preparation and underpinnings, GPO microform storage in libraries, government publications librarians, and the independence of documents collections…

Alliance Building in the Information and Online Database Industry.

ERIC Educational Resources Information Center

Alexander, Johanna Olson

2001-01-01

Presents an analysis of information industry alliance formation using environmental scanning methods. Highlights include why libraries and academic institutions should be interested; a literature review; historical context; industry and market structures; commercial and academic models; trends; and implications for information providers,…

MISR Regional SAMUM Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

Digital Preservation and Metadata: History, Theory, Practice.

ERIC Educational Resources Information Center

Lazinger, Susan S.

This book addresses critical issues of digital preservation, providing guidelines for protecting resources from dealing with obsolescence, to responsibilities, methods of preservation, cost, and metadata formats. It also shows numerous national and international institutions that provide frameworks for digital libraries and archives. The first…

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

2015-10-01

In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

The Digital electronic Guideline Library (DeGeL): a hybrid framework for representation and use of clinical guidelines.

PubMed

Shahar, Yuval; Young, Ohad; Shalom, Erez; Mayaffit, Alon; Moskovitch, Robert; Hessing, Alon; Galperin, Maya

2004-01-01

We propose to present a poster (and potentially also a demonstration of the implemented system) summarizing the current state of our work on a hybrid, multiple-format representation of clinical guidelines that facilitates conversion of guidelines from free text to a formal representation. We describe a distributed Web-based architecture (DeGeL) and a set of tools using the hybrid representation. The tools enable performing tasks such as guideline specification, semantic markup, search, retrieval, visualization, eligibility determination, runtime application and retrospective quality assessment. The representation includes four parallel formats: Free text (one or more original sources); semistructured text (labeled by the target guideline-ontology semantic labels); semiformal text (which includes some control specification); and a formal, machine-executable representation. The specification, indexing, search, retrieval, and browsing tools are essentially independent of the ontology chosen for guideline representation, but editing the semi-formal and formal formats requires ontology-specific tools, which we have developed in the case of the Asbru guideline-specification language. The four formats support increasingly sophisticated computational tasks. The hybrid guidelines are stored in a Web-based library. All tools, such as for runtime guideline application or retrospective quality assessment, are designed to operate on all representations. We demonstrate the hybrid framework by providing examples from the semantic markup and search tools.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

Advanced Data Format (ADF) Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Smith, Matthew; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial. Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: 1) The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its 1/0 software, which handles the actual reading and writing of data from and to external storage media; 2) The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; 3) The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and 4) The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The ADF is a generic database manager with minimal intrinsic capability. It was written for the purpose of storing large numerical datasets in an efficient, platform independent manner. To be effective, it must be used in conjunction with external agreements on how the data will be organized within the ADF database such defined by the SIDS. There are currently 34 user callable functions that comprise the ADF Core library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

The US National Library of Medicine in the 21st century: expanding collections, nontraditional formats, new audiences.

PubMed

Lacroix, Eve-Marie; Mehnert, Robert

2002-09-01

From the early 1960s, the US National Library of Medicine (NLM) has been a leader in applying computer technology to accomplish traditional bibliographic and reference functions. medline, in the early 1970s, was the first large-scale online medical bibliographic reference system. That role has been altered by today's Web environment, which has increased the number and extent of NLM services and the audience for them. The NLM has formally declared that it will seek to serve the general public after over a century of serving the library and medical communities exclusively. In the last several years, many new services have been introduced to fulfil this mandate, including medlineplus and ClinicalTrials.gov. Also a part of the NLM's vision for the 21st century is the need to ensure that the proliferating forms of electronic health information-bibliographic, full text, graphic, audiovisual-are captured and preserved for posterity. A national library such as the NLM has as much an archival responsibility for this electronic information as for centuries-old printed and manuscript historical treasures.

Electronic health record meets digital library: a new environment for achieving an old goal.

PubMed

Humphreys, B L

2000-01-01

Linking the electronic health record to the digital library is a Web-era reformulation of the long-standing informatics goal of seamless integration of automated clinical data and relevant knowledge-based information to support informed decisions. The spread of the Internet, the development of the World Wide Web, and converging format standards for electronic health data and digital publications make effective linking increasingly feasible. Some existing systems link electronic health data and knowledge-based information in limited settings or limited ways. Yet many challenging informatics research problems remain to be solved before flexible and seamless linking becomes a reality and before systems become capable of delivering the specific piece of information needed at the time and place a decision must be made. Connecting the electronic health record to the digital library also requires positive resolution of important policy issues, including health data privacy, government encouragement of high-speed communications, electronic intellectual property rights, and standards for health data and for digital libraries. Both the research problems and the policy issues should be important priorities for the field of medical informatics.

Electronic Health Record Meets Digital Library

PubMed Central

Humphreys, Betsy L.

2000-01-01

Linking the electronic health record to the digital library is a Web-era reformulation of the long-standing informatics goal of seamless integration of automated clinical data and relevant knowledge-based information to support informed decisions. The spread of the Internet, the development of the World Wide Web, and converging format standards for electronic health data and digital publications make effective linking increasingly feasible. Some existing systems link electronic health data and knowledge-based information in limited settings or limited ways. Yet many challenging informatics research problems remain to be solved before flexible and seamless linking becomes a reality and before systems become capable of delivering the specific piece of information needed at the time and place a decision must be made. Connecting the electronic health record to the digital library also requires positive resolution of important policy issues, including health data privacy, government envouragement of high-speed communications, electronic intellectual property rights, and standards for health data and for digital libraries. Both the research problems and the policy issues should be important priorities for the field of medical informatics. PMID:10984463

An object-oriented data reduction system in Fortran

NASA Technical Reports Server (NTRS)

Bailey, J.

1992-01-01

A data reduction system for the AAO two-degree field project is being developed using an object-oriented approach. Rather than use an object-oriented language (such as C++) the system is written in Fortran and makes extensive use of existing subroutine libraries provided by the UK Starlink project. Objects are created using the extensible N-dimensional Data Format (NDF) which itself is based on the Hierarchical Data System (HDS). The software consists of a class library, with each class corresponding to a Fortran subroutine with a standard calling sequence. The methods of the classes provide operations on NDF objects at a similar level of functionality to the applications of conventional data reduction systems. However, because they are provided as callable subroutines, they can be used as building blocks for more specialist applications. The class library is not dependent on a particular software environment thought it can be used effectively in ADAM applications. It can also be used from standalone Fortran programs. It is intended to develop a graphical user interface for use with the class library to form the 2dF data reduction system.

Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes.

PubMed

Uchiyama, Taku; Miyazaki, Kentaro

2010-11-01

A reporter assay-based screening method for enzymes, which we named product-induced gene expression (PIGEX), was developed and used to screen a metagenomic library for amidases. A benzoate-responsive transcriptional activator, BenR, was placed upstream of the gene encoding green fluorescent protein and used as a sensor. Escherichia coli sensor cells carrying the benR-gfp gene cassette fluoresced in response to benzoate concentrations as low as 10 μM but were completely unresponsive to the substrate benzamide. An E. coli metagenomic library consisting of 96,000 clones was grown in 96-well format in LB medium containing benzamide. The library cells were then cocultivated with sensor cells. Eleven amidase genes were recovered from 143 fluorescent wells; eight of these genes were homologous to known bacterial amidase genes while three were novel genes. In addition to their activity toward benzamide, the enzymes were active toward various substrates, including d- and l-amino acid amides, and displayed enantioselectivity. Thus, we demonstrated that PIGEX is an effective approach for screening novel enzymes based on product detection.

Validation of the BUGJEFF311.BOLIB, BUGENDF70.BOLIB and BUGLE-B7 broad-group libraries on the PCA-Replica (H2O/Fe) neutron shielding benchmark experiment

NASA Astrophysics Data System (ADS)

Pescarini, Massimo; Orsi, Roberto; Frisoni, Manuela

2016-03-01

The PCA-Replica 12/13 (H2O/Fe) neutron shielding benchmark experiment was analysed using the TORT-3.2 3D SN code. PCA-Replica reproduces a PWR ex-core radial geometry with alternate layers of water and steel including a pressure vessel simulator. Three broad-group coupled neutron/photon working cross section libraries in FIDO-ANISN format with the same energy group structure (47 n + 20 γ) and based on different nuclear data were alternatively used: the ENEA BUGJEFF311.BOLIB (JEFF-3.1.1) and UGENDF70.BOLIB (ENDF/B-VII.0) libraries and the ORNL BUGLE-B7 (ENDF/B-VII.0) library. Dosimeter cross sections derived from the IAEA IRDF-2002 dosimetry file were employed. The calculated reaction rates for the Rh-103(n,n')Rh-103m, In-115(n,n')In-115m and S-32(n,p)P-32 threshold activation dosimeters and the calculated neutron spectra are compared with the corresponding experimental results.

A Model of RHIC Using the Unified Accelerator Libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilat, F.; Tepikian, S.; Trahern, C. G.

1998-01-01

The Unified Accelerator Library (UAL) is an object oriented and modular software environment for accelerator physics which comprises an accelerator object model for the description of the machine (SMF, for Standard Machine Format), a collection of Physics Libraries, and a Perl inte,face that provides a homo­geneous shell for integrating and managing these components. Currently available physics libraries include TEAPOT++, a collection of C++ physics modules conceptually derived from TEAPOT, and DNZLIB, a differential algebra package for map generation. This software environment has been used to build a flat model of RHIC which retains the hierarchical lat­tice description while assigning specificmore » characteristics to individual elements, such as measured field har­monics. A first application of the model and of the simulation capabilities of UAL has been the study of RHIC stability in the presence of siberian snakes and spin rotators. The building blocks of RHIC snakes and rotators are helical dipoles, unconventional devices that can not be modeled by traditional accelerator phys­ics codes and have been implemented in UAL as Taylor maps. Section 2 describes the RHIC data stores, Section 3 the RHIC SMF format and Section 4 the RHIC spe­cific Perl interface (RHIC Shell). Section 5 explains how the RHIC SMF and UAL have been used to study the RHIC dynamic behavior and presents detuning and dynamic aperture results. If the reader is not familiar with the motivation and characteristics of UAL, we include in the Appendix an useful overview paper. An example of a complete set of Perl Scripts for RHIC simulation can also be found in the Appendix.« less

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

PubMed

Dutheil, Julien; Gaillard, Sylvain; Bazin, Eric; Glémin, Sylvain; Ranwez, Vincent; Galtier, Nicolas; Belkhir, Khalid

2006-04-04

A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/output methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

National Library of Medicine Disaster Information Management Research Center: Establishment and growth, 2008–2010 1

PubMed Central

Love, Cynthia B.; Arnesen, Stacey J.; Phillips, Steven J.

2014-01-01

In 2008, the National Library of Medicine (NLM) established the Disaster Information Management Research Center (DIMRC). Prior to 2008, NLM had a long history of involvement in providing health information for disaster management. Aware of this legacy and moved by the catastrophic aftermath of Hurricane Katrina, the NLM long range plan (Charting a Course for the 21st Century: NLM’s Long Range Plan 2006–2016) called for creation of a center to show “a strong commitment to disaster remediation and to provide a platform for demonstrating how libraries and librarians can be part of the solution to this national problem”. NLM was urged to “ensure continuous access to health information and effective use of libraries and librarians when disasters occur”. In response to this charge, NLM has undertaken substantial efforts to ensure that medical libraries have plans for the continuity of their operations, librarians are trained to understand their roles in preparedness and response, online disaster health information resources are available for many audiences and in multiple formats, and research is conducted on tools to enhance the exchange of critical information during and following disasters. This paper documents the history, goals, initiatives, accomplishments and future plans of the Center. PMID:25324584

The use of mobile technology in health libraries: a summary of a UK-based survey.

PubMed

Chamberlain, David; Elcock, Martin; Puligari, Preeti

2015-12-01

Health libraries have changed over the past fifteen years in the format of the information they provide. This is driven by developments in technology. To conduct a survey of NHS health libraries in the United Kingdom in order to summarise how mobile technologies are being used, how they are promoted and how they are delivered, highlighting good practice and solutions to issues. An online survey was carried out in 2013 and sent to academic and NHS web-based discussion lists. There were 199 responses. Main replies were from large Acute Hospital Trusts. Only 18% of respondents had conducted research into use of mobile technology (MT) within their Trust. Forty per cent of Trusts offered clinical point of care tools, 29% mobile catalogues, and 30% had mobile enabled web sites. Libraries utilised third-party partnerships rather than develop their own applications or tools. Seventy per cent of Trusts promoted new MT services via e-mail. Network restrictions were the main barrier to development as well as finance and expertise. Uptake and development of MT is sporadic and driven by individuals. There is an opportunity for collaboration and sharing resources and expertise. There are benefits to adopting user-friendly resources. © 2015 Health Libraries Group.

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

High-Throughput Method for Ranking the Affinity of Peptide Ligands Selected from Phage Display Libraries

PubMed Central

González-Techera, A.; Umpiérrez-Failache, M.; Cardozo, S.; Obal, G.; Pritsch, O.; Last, J. A.; Gee, S. J.; Hammock, B. D.; González-Sapienza, G.

2010-01-01

The use of phage display peptide libraries allows rapid isolation of peptide ligands for any target selector molecule. However, due to differences in peptide expression and the heterogeneity of the phage preparations, there is no easy way to compare the binding properties of the selected clones, which operates as a major “bottleneck” of the technology. Here, we present the development of a new type of library that allows rapid comparison of the relative affinity of the selected peptides in a high-throughput screening format. As a model system, a phage display peptide library constructed on a phagemid vector that contains the bacterial alkaline phosphatase gene (BAP) was selected with an antiherbicide antibody. Due to the intrinsic switching capacity of the library, the selected peptides were transferred “en masse” from the phage coat protein to BAP. This was coupled to an optimized affinity ELISA where normalized amounts of the peptide–BAP fusion allow direct comparison of the binding properties of hundreds of peptide ligands. The system was validated by plasmon surface resonance experiments using synthetic peptides, showing that the method discriminates among the affinities of the peptides within 3 orders of magnitude. In addition, the peptide–BAP protein can find direct application as a tracer reagent. PMID:18393454

Managing Information Resources: New Directions in State Government.

ERIC Educational Resources Information Center

Caudle, Sharon L.; Marchand, Donald A.

1990-01-01

Describes a national survey of management policies and practices applied to information and information technology in state government. Management approaches and trends are discussed in the areas of data processing, telecommunications, office automation, records management, state library services, policy formation, budgeting and accounting,…

Getting into Children's Video.

ERIC Educational Resources Information Center

Hedges, Michael

1983-01-01

Lists videotape titles for preschoolers through preteens available to libraries in VHS and Beta formats for $100 or less, noting running times, release dates, and prices. Materials are categorized by companies serving educational market and home market, and commercial products found in retail stores are grouped by producer. (EJS)

Write Procedures That Work.

ERIC Educational Resources Information Center

Cubberley, Carol W.

1991-01-01

Discusses written procedures that explain library tasks and describes methods for writing them clearly and coherently. The use of appropriate terminology and vocabulary is discussed; the value of illustrations, typography, and format to enhance the visual effect is explained; the intended audience is considered; and examples are given. (seven…

Office Politics

ERIC Educational Resources Information Center

Storm, Paula; Kelly, Robert; deVries, Susann

2008-01-01

People and organizations are inherently political. Library workplace environments have zones of tension and dynamics just like any corporation, often leading to the formation of political camps. These different cliques influence productivity and work-related issues and, at worst, give meetings the feel of the Camp David negotiations. Politics are…

MISR Regional INTEX-B Map Projection

Atmospheric Science Data Center

2016-09-28

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional GoMACCS Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowen, Benjamin; Ruebel, Oliver; Fischer, Curt Fischer R.

BASTet is an advanced software library written in Python. BASTet serves as the analysis and storage library for the OpenMSI project. BASTet is an integrate framework for: i) storage of spectral imaging data, ii) storage of derived analysis data, iii) provenance of analyses, iv) integration and execution of analyses via complex workflows. BASTet implements the API for the HDF5 storage format used by OpenMSI. Analyses that are developed using BASTet benefit from direct integration with storage format, automatic tracking of provenance, and direct integration with command-line and workflow execution tools. BASTet also defines interfaces to enable developers to directly integratemore » their analysis with OpenMSI's web-based viewing infrastruture without having to know OpenMSI. BASTet also provides numerous helper classes and tools to assist with the conversion of data files, ease parallel implementation of analysis algorithms, ease interaction with web-based functions, description methods for data reduction. BASTet also includes detailed developer documentation, user tutorials, iPython notebooks, and other supporting documents.« less

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

Genotype Specification Language.

PubMed

Wilson, Erin H; Sagawa, Shiori; Weis, James W; Schubert, Max G; Bissell, Michael; Hawthorne, Brian; Reeves, Christopher D; Dean, Jed; Platt, Darren

2016-06-17

We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.

A Survey of Complex Object Technologies for Digital Libraries

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Argue, Brad; Efron, Miles; Denn, Sheila; Pattuelli, Maria Cristina

2001-01-01

Many early web-based digital libraries (DLs) had implicit assumptions reflected in their architecture that the unit of focus in the DL (frequently "reports" or "e-prints") would only be manifested in a single, or at most a few, common file formats such as PDF or PostScript. DLs have now matured to the point where their contents are commonly no longer simple files. Complex objects in DLs have emerged from in response to various requirements, including: simple aggregation of formats and supporting files, bundling additional information to aid digital preservation, creating opaque digital objects for e-commerce applications, and the incorporation of dynamic services with the traditional data files. We examine a representative (but not necessarily exhaustive) number of current and recent historical web-based complex object technologies and projects that are applicable to DLs: Aurora, Buckets, ComMentor, Cryptolopes, Digibox, Document Management Alliance, FEDORA, Kahn-Wilensky Framework Digital Objects, Metadata Encoding & Transmission Standard, Multivalent Documents, Open eBooks, VERS Encapsulated Objects, and the Warwick Framework.

Preservation of Chinese Print Astronomical Literature in the Digital and Network Age

NASA Astrophysics Data System (ADS)

Zhang, J.; Shi, W.

2015-04-01

Over the last few decades, more and more journals and books have been published in both electronic and print formats. Some journals have been digitized retrospectively going back to the first volume of more than a hundred years ago, which benefits researchers and librarians tremendously. As a result, many librarians subscribe to books and journals in both electronic and print versions when possible. In many cases, because of budget shortfalls and the low usage of print materials, many libraries have started to order electronic only. This trend heralds a potential demise of print literature as major library resources and has implications for the library services associated with them. This paper proposes some opinions on this issue. We believe that the librarians should pay attention to and conserve the published astronomical literature, a precious historical and cultural heritage, so that we could hand it down to future generations, just like our predecessors did for us.

DendroPy: a Python library for phylogenetic computing.

PubMed

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

Object-oriented sequence analysis: SCL--a C++ class library.

PubMed

Vahrson, W; Hermann, K; Kleffe, J; Wittig, B

1996-04-01

SCL (Sequence Class Library) is a class library written in the C++ programming language. Designed using object-oriented programming principles, SCL consists of classes of objects performing tasks typically needed for analyzing DNA or protein sequences. Among them are very flexible sequence classes, classes accessing databases in various formats, classes managing collections of sequences, as well as classes performing higher-level tasks like calculating a pairwise sequence alignment. SCL also includes classes that provide general programming support, like a dynamically growing array, sets, matrices, strings, classes performing file input/output, and utilities for error handling. By providing these components, SCL fosters an explorative programming style: experimenting with algorithms and alternative implementations is encouraged rather than punished. A description of SCL's overall structure as well as an overview of its classes is given. Important aspects of the work with SCL are discussed in the context of a sample program.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Kip, Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staley, Martin

2017-09-20

This high-performance ray tracing library provides very fast rendering; compact code; type flexibility through C++ "generic programming" techniques; and ease of use via an application programming interface (API) that operates independently of any GUI, on-screen display, or other enclosing application. Kip supports constructive solid geometry (CSG) models based on a wide variety of built-in shapes and logical operators, and also allows for user-defined shapes and operators to be provided. Additional features include basic texturing; input/output of models using a simple human-readable file format and with full error checking and detailed diagnostics; and support for shared data parallelism. Kip is writtenmore » in pure, ANSI standard C++; is entirely platform independent; and is very easy to use. As a C++ "header only" library, it requires no build system, configuration or installation scripts, wizards, non-C++ preprocessing, makefiles, shell scripts, or external libraries.« less

mzDB: A File Format Using Multiple Indexing Strategies for the Efficient Analysis of Large LC-MS/MS and SWATH-MS Data Sets*

PubMed Central

Bouyssié, David; Dubois, Marc; Nasso, Sara; Gonzalez de Peredo, Anne; Burlet-Schiltz, Odile; Aebersold, Ruedi; Monsarrat, Bernard

2015-01-01

The analysis and management of MS data, especially those generated by data independent MS acquisition, exemplified by SWATH-MS, pose significant challenges for proteomics bioinformatics. The large size and vast amount of information inherent to these data sets need to be properly structured to enable an efficient and straightforward extraction of the signals used to identify specific target peptides. Standard XML based formats are not well suited to large MS data files, for example, those generated by SWATH-MS, and compromise high-throughput data processing and storing. We developed mzDB, an efficient file format for large MS data sets. It relies on the SQLite software library and consists of a standardized and portable server-less single-file database. An optimized 3D indexing approach is adopted, where the LC-MS coordinates (retention time and m/z), along with the precursor m/z for SWATH-MS data, are used to query the database for data extraction. In comparison with XML formats, mzDB saves ∼25% of storage space and improves access times by a factor of twofold up to even 2000-fold, depending on the particular data access. Similarly, mzDB shows also slightly to significantly lower access times in comparison with other formats like mz5. Both C++ and Java implementations, converting raw or XML formats to mzDB and providing access methods, will be released under permissive license. mzDB can be easily accessed by the SQLite C library and its drivers for all major languages, and browsed with existing dedicated GUIs. The mzDB described here can boost existing mass spectrometry data analysis pipelines, offering unprecedented performance in terms of efficiency, portability, compactness, and flexibility. PMID:25505153

Design and clinical evaluation of a high-capacity digital image archival library and high-speed network for the replacement of cinefilm in the cardiac angiography environment

NASA Astrophysics Data System (ADS)

Cusma, Jack T.; Spero, Laurence A.; Groshong, Bennett R.; Cho, Teddy; Bashore, Thomas M.

1993-09-01

An economical and practical digital solution for the replacement of 35 mm cine film as the archive media in the cardiac x-ray imaging environment has remained lacking to date due to the demanding requirements of high capacity, high acquisition rate, high transfer rate, and a need for application in a distributed environment. A clinical digital image library and network based on the D2 digital video format has been installed in the Duke University Cardiac Catheterization Laboratory. The system architecture includes a central image library with digital video recorders and robotic tape retrieval, three acquisition stations, and remote review stations connected via a serial image network. The library has a capacity for over 20,000 Gigabytes of uncompressed image data, equivalent to records for approximately 20,000 patients. Image acquisition in the clinical laboratories is via a real-time digital interface between the digital angiography system and a local digital recorder. Images are transferred to the library over the serial network at a rate of 14.3 Mbytes/sec and permanently stored for later review. The image library and network are currently undergoing a clinical comparison with cine film for visual and quantitative assessment of coronary artery disease. At the conclusion of the evaluation, the configuration will be expanded to include four additional catheterization laboratories and remote review stations throughout the hospital.

A Digital Library for the National Advisory Committee for Aeronautics

NASA Technical Reports Server (NTRS)

Nelson, Michael L.

1999-01-01

We describe the digital library (DL) for the National Advisory Committee for Aeronautics (NACA), the NACA Technical Report Server (NACATRS). The predecessor organization for the National Aeronautics and Space Administration (NASA), NACA existed from 1915 until 1958. The primary manifestation of NACA's research was the NACA report series. We describe the process of converting this collection of reports to digital format and making it available on the World Wide Web (WWW) and is a node in the NASA Technical Report Server (NTRS). We describe the current state of the project, the resulting DL technology developed from the project, and the future plans for NACATRS.

voevent-parse: Parse, manipulate, and generate VOEvent XML packets

NASA Astrophysics Data System (ADS)

Staley, Tim D.

2014-11-01

voevent-parse, written in Python, parses, manipulates, and generates VOEvent XML packets; it is built atop lxml.objectify. Details of transients detected by many projects, including Fermi, Swift, and the Catalina Sky Survey, are currently made available as VOEvents, which is also the standard alert format by future facilities such as LSST and SKA. However, working with XML and adhering to the sometimes lengthy VOEvent schema can be a tricky process. voevent-parse provides convenience routines for common tasks, while allowing the user to utilise the full power of the lxml library when required. An earlier version of voevent-parse was part of the pysovo (ascl:1411.002) library.

The Creative Deliverable: A Short Communication

ERIC Educational Resources Information Center

Hartel, Jenna; Noone, Rebecca; Oh, Christie

2017-01-01

This paper encourages educators in library and information science (LIS) to adopt the "creative deliverable," that is, an assignment that gives students the freedom to display their understanding of course material in an almost unrestricted range of alternative formats and genres, while retaining some key features of traditional…

A Salute to a Leader: ARL's Assessment Protocol Initiatives

ERIC Educational Resources Information Center

Heath, Fred

2009-01-01

This brief salute to Duane Webster and his defining role over the past several decades at the Association of Research Libraries (ARL) focuses on his formative role in defining and evolving the assessment protocols employed by both the association and the profession. (Contains 8 notes.)

Digitized Archival Primary Sources in STEM: A Selected Webliography

ERIC Educational Resources Information Center

Jankowski, Amy

2017-01-01

Accessibility and findability of digitized archival resources can be a challenge, particularly for students or researchers not familiar with archival formats and digital interfaces, which adhere to different descriptive standards than more widely familiar library resources. Numerous aggregate archival collection databases exist, which provide a…

Betty Petersen Memorial Library - NCWCP Publications - NWS

Science.gov Websites

Resources NCEP Office Notes IT Resources Request an item* University of Maryland Research Affiliate Contact for Environmental Prediction (NCEP) NESDIS Center for Satellite Applications & Research (STAR (*revised) (.PDF file) 29 1969 1990* Automation Division Staff NMC Format For Observational Data (ADP

Choosing the Right Database Management Program.

ERIC Educational Resources Information Center

Vockell, Edward L.; Kopenec, Donald

1989-01-01

Provides a comparison of four database management programs commonly used in schools: AppleWorks, the DOS 3.3 and ProDOS versions of PFS, and MECC's Data Handler. Topics discussed include information storage, spelling checkers, editing functions, search strategies, graphs, printout formats, library applications, and HyperCard. (LRW)

When Violence Threatens the Workplace: Personnel Issues.

ERIC Educational Resources Information Center

Willits, Robert L.

1997-01-01

Discusses violence in the workplace and suggests a three-tier approach to dealing with violence in libraries that focuses on personnel issues: (1) preventive measures, including applicant screening, supervisory training, and employee assistance programs; (2) threat management, including policy formation and legal action; and (3) crisis/post-trauma…

Best Audiobooks of 2007

ERIC Educational Resources Information Center

Burns, Ann

2008-01-01

Heard any good books lately? Apparently, lots of people are listening. According to a survey conducted by the Audio Publishers Association, annual audiobook sales are now estimated at $923 million. Customers find books at libraries, retail stores, and through downloading, which is becoming the fastest-growing audiobook format. This article…

Film versus Video: Comparing the Forms.

ERIC Educational Resources Information Center

Kreamer, Jean T.

1985-01-01

Compares specific aspects of 16mm film and the videocassette that should be considered in making media software and hardware purchase decisions for library media collections: aesthetics and intended audience size, compatibility and format, costs, copyright, market trends, and major advantages and disadvantages. A four-item bibliography is…

Reference Manual for Machine-Readable Bibliographic Descriptions. Second Revised Edition.

ERIC Educational Resources Information Center

Dierickx, H., Ed.; Hopkinson, A., Ed.

A product of the UNISIST International Centre for Bibliographic Descriptions (UNIBIB), this reference manual presents a standardized communication format for the exchange of machine-readable bibliographic information between bibliographic databases or other types of bibliographic information services, including libraries. The manual is produced in…

Programmatic access to data and information at the IRIS DMC via web services

NASA Astrophysics Data System (ADS)

Weertman, B. R.; Trabant, C.; Karstens, R.; Suleiman, Y. Y.; Ahern, T. K.; Casey, R.; Benson, R. B.

2011-12-01

The IRIS Data Management Center (DMC) has developed a suite of web services that provide access to the DMC's time series holdings, their related metadata and earthquake catalogs. In addition, services are available to perform simple, on-demand time series processing at the DMC prior to being shipped to the user. The primary goal is to provide programmatic access to data and processing services in a manner usable by and useful to the research community. The web services are relatively simple to understand and use and will form the foundation on which future DMC access tools will be built. Based on standard Web technologies they can be accessed programmatically with a wide range of programming languages (e.g. Perl, Python, Java), command line utilities such as wget and curl or with any web browser. We anticipate these services being used for everything from simple command line access, used in shell scripts and higher programming languages to being integrated within complex data processing software. In addition to improving access to our data by the seismological community the web services will also make our data more accessible to other disciplines. The web services available from the DMC include ws-bulkdataselect for the retrieval of large volumes of miniSEED data, ws-timeseries for the retrieval of individual segments of time series data in a variety of formats (miniSEED, SAC, ASCII, audio WAVE, and PNG plots) with optional signal processing, ws-station for station metadata in StationXML format, ws-resp for the retrieval of instrument response in RESP format, ws-sacpz for the retrieval of sensor response in the SAC poles and zeros convention and ws-event for the retrieval of earthquake catalogs. To make the services even easier to use, the DMC is developing a library that allows Java programmers to seamlessly retrieve and integrate DMC information into their own programs. The library will handle all aspects of dealing with the services and will parse the returned data. By using this library a developer will not need to learn the details of the service interfaces or understand the data formats returned. This library will be used to build the software bridge needed to request data and information from within MATLAB°. We also provide several client scripts written in Perl for the retrieval of waveform data, metadata and earthquake catalogs using command line programs. For more information on the DMC's web services please visit http://www.iris.edu/ws/

GNU Data Language (GDL) - a free and open-source implementation of IDL

NASA Astrophysics Data System (ADS)

Arabas, Sylwester; Schellens, Marc; Coulais, Alain; Gales, Joel; Messmer, Peter

2010-05-01

GNU Data Language (GDL) is developed with the aim of providing an open-source drop-in replacement for the ITTVIS's Interactive Data Language (IDL). It is free software developed by an international team of volunteers led by Marc Schellens - the project's founder (a list of contributors is available on the project's website). The development is hosted on SourceForge where GDL continuously ranks in the 99th percentile of most active projects. GDL with its library routines is designed as a tool for numerical data analysis and visualisation. As its proprietary counterparts (IDL and PV-WAVE), GDL is used particularly in geosciences and astronomy. GDL is dynamically-typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, interaction with host OS and data input/output. GDL supports several data formats such as netCDF, HDF4, HDF5, GRIB, PNG, TIFF, DICOM, etc. Graphical output is handled by X11, PostScript, SVG or z-buffer terminals, the last one allowing output to be saved in a variety of raster graphics formats. GDL is an incremental compiler with integrated debugging facilities. It is written in C++ using the ANTLR language-recognition framework. Most of the library routines are implemented as interfaces to open-source packages such as GNU Scientific Library, PLPlot, FFTW, ImageMagick, and others. GDL features a Python bridge (Python code can be called from GDL; GDL can be compiled as a Python module). Extensions to GDL can be written in C++, GDL, and Python. A number of open software libraries written in IDL, such as the NASA Astronomy Library, MPFIT, CMSVLIB and TeXtoIDL are fully or partially functional under GDL. Packaged versions of GDL are available for several Linux distributions and Mac OS X. The source code compiles on some other UNIX systems, including BSD and OpenSolaris. The presentation will cover the current status of the project, the key accomplishments, and the weaknesses - areas where contributions and users' feedback are welcome! While still being in beta-stage of development, GDL proved to be a useful tool for classroom work on data analysis. Its usage for teaching meteorological-data processing at the University of Warsaw will serve as an example.

Using graph approach for managing connectivity in integrative landscape modelling

NASA Astrophysics Data System (ADS)

Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger

2013-04-01

In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). OpenFLUID-landr library has been developed in order i) to be used with no GIS expert skills needed (common gis formats can be read and simplified spatial management is provided), ii) to easily develop adapted rules of landscape discretization and graph creation to follow spatialized model requirements and iii) to allow model developers to manage dynamic and complex spatial topology. Graph management in OpenFLUID are shown with i) examples of hydrological modelizations on complex farmed landscapes and ii) the new implementation of Geo-MHYDAS tool based on the OpenFLUID-landr library, which allows to discretize a landscape and create graph structure for the MHYDAS model requirements.

Issues for bringing digital libraries into public use

NASA Technical Reports Server (NTRS)

Flater, David W.; Yesha, Yelena

1993-01-01

In much the same way that the field of artificial intelligence produced a cult which fervently believed that computers would soon think like human beings, the existence of electronic books has resurrected the paperless society as a utopian vision to some, an apocalyptic horror to others. In this essay we have attempted to provide realistic notions of what digital libraries are likely to become if they are a popular success. E-books are capable of subsuming most of the media we use today and have the potential for added functionality by being interactive. The environmental impact of having millions more computers will be offset to some degree, perhaps even exceeded, by the fact that televisions, stereos, VCR's, CD players, newspapers, magazines, and books will become part of the computer system or be made redundant. On the whole, large-scale use of digital libraries is likely to be a winning proposition. Whether or not this comes to pass depends on the directions taken by today's researchers and software developers. By involving the public, the effort being put into digital libraries can be leveraged into something which is big enough to make a real change for the better. If digital libraries remain the exclusive property of government, universities, and large research firms, then large parts of the world will remain without digital libraries for years to come, just as they have remained without digital phone service for far too long. If software companies try to scuttle the project by patenting crucial algorithms and using proprietary data formats, all of us will suffer. Let us reverse the errors of the past and create a truly open digital library system.

Synthesis of small combinatorial libraries of natural products: identification and quantification of new long-chain 3-methyl-2-alkanones from the root essential oil of Inula helenium L. (Asteraceae).

PubMed

Radulović, Niko S; Denić, Marija S; Stojanović-Radić, Zorica Z

2014-01-01

Recently, a potent anti-staphylococcal activity of Inula helenium L. (Asteraceae) root essential oil was reported. Also, bioassay guided fractionation of the oil pointed to eudesmane sesquiterpene lactones and a series of unidentified constituents as the main carriers of the observed activity. To identify nine new constituents (long-chain 3-methyl-2-alkanones) from a fraction of this root essential oil with a low minimum inhibitory concentration value (0.8 µg/mL) by employing a synthetic methodology that leads to the formation of a small combinatorial library of these compounds. The identity of these constituents was inferred from mass spectral fragmentation patterns and GC retention data. A library of 3-methyl-2-alkanones (C11 -C19 homologous series) was synthesised in three steps starting from methyl acetoacetate and the corresponding alkyl halides. The synthetic library was also screened for in vitro anti-microbial activity. Gas chromatographic analyses of I. helenium essential oil samples with spiked compounds from the synthesised library corroborated the tentative identifications of the long-chain 3-methyl-2-alkanones. The availability of these anti-microbial compounds from this library made it possible to construct GC/FID calibration curves and determine their content in the plant material: 0.08 - 24.2 mg/100 g of dry roots. The small combinatorial library approach enabled the first unequivocal identification of long-chain 3-methyl-2-alkanones as plant secondary metabolites, and, also, allowed determination of not only a single compound and biological properties, but those of a group of structurally related compounds. Copyright © 2013 John Wiley & Sons, Ltd.

MATH77 - A LIBRARY OF MATHEMATICAL SUBPROGRAMS FOR FORTRAN 77, RELEASE 4.0

NASA Technical Reports Server (NTRS)

Lawson, C. L.

1994-01-01

MATH77 is a high quality library of ANSI FORTRAN 77 subprograms implementing contemporary algorithms for the basic computational processes of science and engineering. The portability of MATH77 meets the needs of present-day scientists and engineers who typically use a variety of computing environments. Release 4.0 of MATH77 contains 454 user-callable and 136 lower-level subprograms. Usage of the user-callable subprograms is described in 69 sections of the 416 page users' manual. The topics covered by MATH77 are indicated by the following list of chapter titles in the users' manual: Mathematical Functions, Pseudo-random Number Generation, Linear Systems of Equations and Linear Least Squares, Matrix Eigenvalues and Eigenvectors, Matrix Vector Utilities, Nonlinear Equation Solving, Curve Fitting, Table Look-Up and Interpolation, Definite Integrals (Quadrature), Ordinary Differential Equations, Minimization, Polynomial Rootfinding, Finite Fourier Transforms, Special Arithmetic , Sorting, Library Utilities, Character-based Graphics, and Statistics. Besides subprograms that are adaptations of public domain software, MATH77 contains a number of unique packages developed by the authors of MATH77. Instances of the latter type include (1) adaptive quadrature, allowing for exceptional generality in multidimensional cases, (2) the ordinary differential equations solver used in spacecraft trajectory computation for JPL missions, (3) univariate and multivariate table look-up and interpolation, allowing for "ragged" tables, and providing error estimates, and (4) univariate and multivariate derivative-propagation arithmetic. MATH77 release 4.0 is a subroutine library which has been carefully designed to be usable on any computer system that supports the full ANSI standard FORTRAN 77 language. It has been successfully implemented on a CRAY Y/MP computer running UNICOS, a UNISYS 1100 computer running EXEC 8, a DEC VAX series computer running VMS, a Sun4 series computer running SunOS, a Hewlett-Packard 720 computer running HP-UX, a Macintosh computer running MacOS, and an IBM PC compatible computer running MS-DOS. Accompanying the library is a set of 196 "demo" drivers that exercise all of the user-callable subprograms. The FORTRAN source code for MATH77 comprises 109K lines of code in 375 files with a total size of 4.5Mb. The demo drivers comprise 11K lines of code and 418K. Forty-four percent of the lines of the library code and 29% of those in the demo code are comment lines. The standard distribution medium for MATH77 is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 9track 1600 BPI magnetic tape in VAX BACKUP format and a TK50 tape cartridge in VAX BACKUP format. An electronic copy of the documentation is included on the distribution media. Previous releases of MATH77 have been used over a number of years in a variety of JPL applications. MATH77 Release 4.0 was completed in 1992. MATH77 is a copyrighted work with all copyright vested in NASA.

Sideloading - Ingestion of Large Point Clouds Into the Apache Spark Big Data Engine

NASA Astrophysics Data System (ADS)

Boehm, J.; Liu, K.; Alis, C.

2016-06-01

In the geospatial domain we have now reached the point where data volumes we handle have clearly grown beyond the capacity of most desktop computers. This is particularly true in the area of point cloud processing. It is therefore naturally lucrative to explore established big data frameworks for big geospatial data. The very first hurdle is the import of geospatial data into big data frameworks, commonly referred to as data ingestion. Geospatial data is typically encoded in specialised binary file formats, which are not naturally supported by the existing big data frameworks. Instead such file formats are supported by software libraries that are restricted to single CPU execution. We present an approach that allows the use of existing point cloud file format libraries on the Apache Spark big data framework. We demonstrate the ingestion of large volumes of point cloud data into a compute cluster. The approach uses a map function to distribute the data ingestion across the nodes of a cluster. We test the capabilities of the proposed method to load billions of points into a commodity hardware compute cluster and we discuss the implications on scalability and performance. The performance is benchmarked against an existing native Apache Spark data import implementation.

IFLA General Conference, 1986. Bibliographic Control Division. Section: Cataloguing. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, The Hague (Netherlands).

Papers on cataloging which were presented at the 1986 International Federation of Library Associations (IFLA) conference include: (1) "Cataloging of Government Documents in the Age of Automation" (Chong Y. Yoon, United States), which discusses the use of MARC (Machine-Readable Cataloging) formats to integrate government documents into…

The Commission on Preservation and Access Newsletter. 1994.

ERIC Educational Resources Information Center

Commission on Preservation and Access Newsletter, 1994

1994-01-01

The Commission on Preservation and Access was established in 1986 to foster and support collaboration among libraries and allied organizations in order to ensure the preservation of the published and documentary record in all formats and to provide enhanced access to scholarly information. The Commission's newsletter keeps the preservation and…

CD-ROM in a High School Library Media Center.

ERIC Educational Resources Information Center

Barlow, Diane; And Others

1987-01-01

Describes the experiences of high school students using microcomputers to access an electronic version of an encyclopedia in the school's media center. The topics discussed include hardware and software requirements of the CD-ROM format, information seeking strategies and problems observed, student satisfaction with the system, and recommendations…

Transitions to Digital Media: Are School Libraries on the Way Out?

ERIC Educational Resources Information Center

McLester, Susan

2013-01-01

Enlightened administrators realize that school librarians still play a pivotal role for students, guiding them through search processes and helping them find appropriate, reliable, vetted resources in print and digital format for research and other classroom projects. This article describes how important the role of information navigator is…

Computerized Serial Processing System at the University of California, Berkeley

ERIC Educational Resources Information Center

Silberstein, Stephen M.

1975-01-01

The extreme flexibility of the MARC format coupled with the simplicity of a batch-oriented processing system centered around a sequential master file has enabled the University of California, Berkeley, library to gradually build an unusually large serials data base in support of both technical and public services. (Author)

Steps toward a Formative Evaluation of NSDL. Technical Report

ERIC Educational Resources Information Center

Bikson, Tora K.; Kalra, Nidhi; Galway, Lionel A.; Agnew, Grace

2011-01-01

The National Science Foundation's (NSF) National Science Digital Library/Distributed Learning (NSDL) program turned 10 years old in 2010. This report presents results of a preliminary program evaluation carried out by RAND and is organized around three principal goals: (1) Provide an initial evaluation of NSDL based on existing information…

May We Help You Find Something? AskNSDL!

ERIC Educational Resources Information Center

Silverstein, Joanne

2003-01-01

Explains the digital reference service AskNSDL that was developed for the National Science Digital Library (NSDL). Discusses tools used to design the service, including QABuilder software; QuIP (Question Interchange Profile) metadata format standard; GEM (Gateway to Educational Materials) cataloging tool; and the AskERIC question and answer…

Heirs of Osler: medical bibliophiles in America.

PubMed

Saffron, M H

1992-11-01

An heir is one who appears to acquire a trait from a predecessor or carries on his tradition. The author presents details about the great bibliophiles who received their stimulus from William Osler, his associates, or his writings. William Osler influenced the formation of private libraries in the United States.

SPEAKEASY HELP documents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fink, J.K.

1972-07-01

The HELP documents provide SPEAKEASY users with concise definitions of most of the words available in the current processors. In this report, the documents are given in a variety of formats to enable one to find specific information quickly. The bulk of this report consists of computer read-out of the HELP library via SPEAKEASY.

Successful Principles for Collaboration: Formation of the IAIMS Consortium.

ERIC Educational Resources Information Center

Stead, William W.; And Others

1991-01-01

Six universities collaborated in developing an integrated academic information management system (IAIMS) to manage data and information as a shared resource and to bring together resources for timely decision making. The program assists institutions in linking their library systems and other information systems to support education, research,…

Performance Measurement for Public Services in Academic and Research Libraries. Occasional Paper Number #9.

ERIC Educational Resources Information Center

Cronin, Mary J.

This paper defines performance measurement as the clarification of objectives and standards, identification of key activities, data collection and analysis, and formative evaluation of services. It then examines some of the factors involved in using performance measurement to evaluate public services activities, and analyzes performance…

Secure Channel Establishment in Disadvantaged Networks: TLS Optimization Using Intercepting Proxies

DTIC Science & Technology

2009-08-18

50 4.1.2 Link Emulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 4.1.3 Openssl ...59 5 5.3 Acquired Skills . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 5.3.1 Openssl ...an openssl library [4], which is designed to work with differing certificate formats. 1.2.3.4 TLS Handshakes A TLS connection begins with a handshake

Form Subdivisions: Their Identification and Use in LCSH.

ERIC Educational Resources Information Center

O'Neill, Edward T.; Chan, Lois Mai; Childress, Eric; Dean, Rebecca; El-Hoshy, Lynn M.; Vizine-Goetz, Diane

2001-01-01

Discusses form subdivisions as part of Library of Congress Subject Headings (LCSH) and the MARC format, which did not have a separate subfield code to identify form subdivisions. Describes the development of an algorithm to identify form subdivisions and reports results of an evaluation of the algorithm. (LRW)

Assessing the Virtual Depository Program: The Arizona Experience

ERIC Educational Resources Information Center

Rawan, Atifa; Malone, Cheryl Knott; Bender, Laura J.

2004-01-01

A decade after passage of the Government Printing Office Electronic Information Access Enhancement Act of 1993, a pilot study at the University of Arizona examined the impact of one selective depository library's decision to select, whenever possible, Web-based government information instead of tangible formats such as print and microfiche. The…

37 CFR 201.40 - Exemption to prohibition against circumvention.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Exemption to prohibition against circumvention. 201.40 Section 201.40 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY... operate. (c) Definition. “Specialized format,” “digital text” and “authorized entities” shall have the...

Enhancing Your CD-ROM Services with Signage Systems.

ERIC Educational Resources Information Center

Ekhaml, Leticia

1994-01-01

Describes how to use effective signage, or visual guidance, for more efficient use of CD-ROM technology in elementary and secondary school library media centers. Setting CD-ROM policies and procedures is considered; the use of posters, brochures, flowcharts, and other formats is discussed; and examples are included. (LRW)

Publishing Trends within State Government: The Situation in North Carolina

ERIC Educational Resources Information Center

Martin, Kristin E.

2004-01-01

The State Library of North Carolina is responsible for ensuring public access to North Carolina state government publications and maintaining a permanent state documents depository collections. Over the last 7 years, state agencies have increasingly disseminated information in digital formats via the Internet, posing challenges for the State…

Kardex Quadrangle Overlays - www.arlis.org

Science.gov Websites

Wild & Scenic Rivers About Contacts Partner Libraries Policies Administrative Records Challenged Records Challenged Materials Circulation Code of Conduct Conference Room Conference Room Form Internet Use /AK/AE-03/003. This page links to records in jpg graphics format. The images in this collection are

Print versus electronic journals: a preliminary investigation into the effect of journal format on research processes*

PubMed Central

Sathe, Nila A.; Grady, Jenifer L.; Giuse, Nunzia B.

2002-01-01

Purpose: To begin investigating the impact of electronic journals on research processes such as information seeking, the authors conducted a pilot journal-use study to test the hypothesis that patrons use print and electronic journals differently. Methodology: We placed fifteen high-use print titles also available in electronic format behind the circulation desk; patrons were asked to complete a survey upon requesting a journal. We also conducted a parallel survey of patrons using library computers. Both surveys asked patrons to identify themselves by user category and queried them about their journal use. Results: During the month-long study, patrons completed sixty-nine surveys of electronic and ninety surveys of print journal use. Results analysis indicated that fellows, students, and residents preferred electronic journals, and faculty preferred print journals. Patrons used print journals for reading articles and scanning contents; they employed electronic journals for printing articles and checking references. Users considered electronic journals easier to access and search than print journals; however, they reported that print journals had higher quality text and figures. Discussion/Conclusion: This study is an introductory step in examining how electronic journals affect research processes. Our data revealed that there were distinct preferences in format among categories. In addition to collection management implications for libraries, these data also have implications for publishers and educators; current electronic formats do not facilitate all types of uses and thus may be changing learning patterns as well. PMID:11999183