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http://www.debian.org

Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.

Proper citation: Debian (RRID:SCR_006638) Copy   

•   Source: SciCrunch Registry

http://neuro.debian.net/

Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.

Proper citation: neurodebian (RRID:SCR_004401) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/node/960

Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).

Proper citation: FreeContact (RRID:SCR_016113) Copy   

•   Source: SciCrunch Registry

http://matrixdb.univ-lyon1.fr/

Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.

Proper citation: MatrixDB (RRID:SCR_001727) Copy   

•   Source: SciCrunch Registry

http://www.biocatalogue.org/

Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.

Proper citation: Biocatalogue - The Life Science Web Services Registry (RRID:SCR_001679) Copy   

•   Source: SciCrunch Registry

http://tango.crg.es/

A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.

Proper citation: TANGO (RRID:SCR_001770) Copy   

•   Source: SciCrunch Registry

http://cufflinks.cbcb.umd.edu/

Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.

Proper citation: Cuffdiff (RRID:SCR_001647) Copy   

•   Source: SciCrunch Registry

https://www.metabase.com/

User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities.

Proper citation: MetaBase (RRID:SCR_001762) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pennseq/

Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.

Proper citation: PennSeq (RRID:SCR_001763) Copy   

•   Source: SciCrunch Registry

http://www.chilibot.net/

Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation

Proper citation: Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) Copy   

•   Source: SciCrunch Registry

http://www.phosphosite.org

A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy   

•   Source: SciCrunch Registry

http://www.r-project.org/

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy   

•   Source: SciCrunch Registry

https://github.com/benedictpaten/pecan

A Java consistency based multiple sequence alignment software program.

Proper citation: Pecan (RRID:SCR_001909) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/denovoassembler/files/

Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

Proper citation: Ray (RRID:SCR_001916) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/gatk/

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Proper citation: GATK (RRID:SCR_001876) Copy   

•   Source: SciCrunch Registry

http://www.agcol.arizona.edu/software/tcw/

Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.

Proper citation: TCW (RRID:SCR_001875) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

http://www.myexperiment.org/

Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

Proper citation: myExperiment (RRID:SCR_001795) Copy   

•   Source: SciCrunch Registry

https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

•   Source: SciCrunch Registry

https://github.com/nicolazzie/AffyPipe

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

Proper citation: AffyPipe (RRID:SCR_002032) Copy   

•   Source: SciCrunch Registry