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http://www.upc.edu/?set_language=en

A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER).

Proper citation: Polytechnic University of Catalonia; Barcelona; Spain (RRID:SCR_000252) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmato/files/?source=navbar

A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.

Proper citation: GMATo (RRID:SCR_000165) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/resources/data-space/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.

Repository for sharing of neuroscience data, text, images, sounds, movies, models and simulations.

Proper citation: INCF Dataspace (RRID:SCR_000158) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Proper citation: DESeq (RRID:SCR_000154) Copy   

•   Source: SciCrunch Registry

https://github.com/davidliwei/RNASeqReadSimulator

A software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.

Proper citation: RNASeqReadSimulator (RRID:SCR_000270) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/glide

Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

Proper citation: Glide (RRID:SCR_000187) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/modent/

A computational tool that reconstructs gene regulatory networks from high throughput experimental data.

Proper citation: MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.

Proper citation: GOLD (RRID:SCR_000188) Copy   

•   Source: SciCrunch Registry

https://omictools.com/context-likelihood-of-relatedness-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.

Proper citation: Context Likelihood of Relatedness (RRID:SCR_000216) Copy   

•   Source: SciCrunch Registry

http://www.csir.co.za/

A leading scientific and technology research, development and implementation organization in Africa that undertakes directed research and development for socio-economic growth and improving the quality of life of South African citizens.

Proper citation: Council for Scientific and Industrial Research; Gauteng; South Africa (RRID:SCR_000214) Copy   

•   Source: SciCrunch Registry

http://www.cdisc.org/

A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Proper citation: Clinical Data Interchange Standards Consortium (RRID:SCR_000219) Copy   

•   Source: SciCrunch Registry

https://github.com/vahuynh/dynGENIE3

An algorithm for the inference of gene regulatory networks from expression data.

Proper citation: GENIE3 (RRID:SCR_000217) Copy   

•   Source: SciCrunch Registry

http://bonneaulab.bio.nyu.edu/networks.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Inferelator (RRID:SCR_000218) Copy   

•   Source: SciCrunch Registry

http://discover.nci.nih.gov/gominer/GoCommandWebInterface.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

Proper citation: High-Throughput GoMiner (RRID:SCR_000173) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/c3net/index.html

Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.

Proper citation: c3net (RRID:SCR_000212) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

http://ccd.biocuckoo.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites.

Proper citation: GPS-Calpain Cleavage Detector (RRID:SCR_000202) Copy   

•   Source: SciCrunch Registry

http://www.themmrf.org/

Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer.

Proper citation: Multiple Myeloma Research Foundation (RRID:SCR_000207) Copy   

•   Source: SciCrunch Registry

http://ribopicker.sourceforge.net/

Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Proper citation: riboPicker (RRID:SCR_000360) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry