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http://www.cdlib.org/

One of the world''s largest digital research libraries that changed the ways that faculty, students, and researchers discover and access information using innovative technology to connect content and communities in ways that enhance teaching, learning, and research. In partnership with the UC libraries, the CDL has continually broken new ground by developing systems linking their users to the vast print and online collections within UC and beyond. Building on the foundations of the Melvyl Catalog, they developed one of the largest online library catalogs in the country. They saved the University millions of dollars by facilitating the co-investment and sharing of materials and services used by libraries across the UC system. They work in partnership with campuses to bring the treasures of their libraries, museums, and cultural heritage organizations to the world. And they continue to explore how services such as digital curation, scholarly publishing, archiving and preservation support research throughout the information lifecycle.

Proper citation: California Digital Library (RRID:SCR_006481) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MethylSeekR.html

A software package for the discovery of regulatory regions from Bis-seq data.

Proper citation: MethylSeekR (RRID:SCR_006513) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

Proper citation: NCBI (RRID:SCR_006472) Copy   

•   Source: SciCrunch Registry

http://n2t.net/ezid

A production service that gives researchers the ability to create and manage long-term identifiers so that they can to track usage, get credit for their work, share their data, and have the data reused for additional research. As a result, EZID identifiers also make it possible to increase citations, to build on previous work, to conduct new research, and avoid duplicating previous efforts. EZID identifiers provide a simple but powerful way to track research materials, including datasets, throughout their life cycle. In this way, researchers can share their data, get more citations, and track their results.

Proper citation: EZID (RRID:SCR_006473) Copy   

•   Source: SciCrunch Registry

http://f1000.com/

Service that identifies and evaluates the most important articles in biology and medical research publications. The selection process comprises a peer-nominated global ''Faculty'' of the world''s leading scientists and clinicians who rate the best of the articles they read and explain their importance. Faculty Members and their evaluations are organized into over 40 Faculties (subjects), which are further subdivided into over 300 Sections. On average, 1500 new evaluations are published each month; this corresponds to approximately the top 2% of all published articles in the biological and medical sciences. F1000 is a subscription service paid for by academic and corporate institutions. Users at subscribing institutions automatically receive full access to the F1000 service when using internet facilities provided by their institution.

Proper citation: F1000: Faculty of 1000 Post-Publication Peer Review (RRID:SCR_006537) Copy   

•   Source: SciCrunch Registry

http://www.tdt.com/

Commercial organization that provides products for basic and applied research in the neurophysiology, hearing, and speech sciences as well as for general data acquisition applications. It offers a complete line of modular DSP-based data acquisition and stimulus generation systems, ranging in complexity from a simple audio stimulator to a complete multichannel sensory and behavioral neurophysiology system for awake, behaving subjects.

Proper citation: Tucker-Davis Technologies (RRID:SCR_006495) Copy   

•   Source: SciCrunch Registry

http://www.asm.org/

The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators. Eligibility for Full Membership is open to any person who is interested in microbiology and holds at least a bachelor''s degree or equivalent experience in microbiology or related field. Many members hold advanced degrees, including a large number at the master''s, PhD, ScD, DrPH and MD level. A regularly matriculated student of microbiology or a related field is eligible to become a student member. There are also separate membership categories for postdoctoral fellows and for transitional scientists in the early years of a career. Microbiologists study microbes--bacteria, viruses, rickettsiae, mycoplasma, fungi, algae and protozoa--some of which cause diseases, but many of which contribute to the balance of nature or are otherwise beneficial. Microbiological research includes infectious diseases, recombinant DNA technology, alternative methods of energy production and waste recycling, new sources of food, new drug development, and the etiology of sexually transmitted diseases, among other areas. Microbiology is also concerned with environmental problems and industrial processes. Microbiology boasts some of the most illustrious names in the annals of science--Pasteur, Koch, Fleming, Leeuwenhoek, Lister, Jenner and Salk--and some of the greatest achievements for mankind. Within the 20th century, a third of all Nobel Prizes in Physiology or Medicine have been bestowed upon microbiologists. The mission of the American Society for Microbiology is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well being worldwide. To achieve these goals, ASM will: * Support programs of education, training and public information; * Publish journals and books; convene meetings, workshops and colloquia; * Promote the contributions and promise of the microbiological sciences; * Recognize achievement and distinction among its practitioners; * Set standards of ethical and professional behavior.

Proper citation: American Society for Microbiology (RRID:SCR_006551) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/casper.html

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

https://www.nimhgenetics.org/

Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.

Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy   

•   Source: SciCrunch Registry

http://www.prosci-inc.com/

An Antibody supplier

Proper citation: ProSci (RRID:SCR_006609) Copy   

•   Source: SciCrunch Registry

https://www.progen.com/

Antibody and density gradient media supplier.

Proper citation: Progen (RRID:SCR_006726) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/splicetrap/

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.

Proper citation: SpliceTrap (RRID:SCR_006728) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/bedtools2

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Proper citation: BEDTools (RRID:SCR_006646) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/niftysim/

A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages.

Proper citation: NiftySim (RRID:SCR_006591) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/LexEVS/LexGrid

LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: LexGrid (RRID:SCR_006627) Copy   

•   Source: SciCrunch Registry

http://www.alexaplatform.org/alexa_seq/index.htm

A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''.

Proper citation: ALEXA-Seq (RRID:SCR_006700) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

Proper citation: ChIPXpress (RRID:SCR_006653) Copy   

•   Source: SciCrunch Registry

https://www.promega.com/

An Antibody supplier

Proper citation: Promega (RRID:SCR_006724) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/webmill/

Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function.

Proper citation: Web Game for Collaborative Labeling (RRID:SCR_006685) Copy   

•   Source: SciCrunch Registry