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http://www.paradyn.org/mrnet/

A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication.

Proper citation: MRNet (RRID:SCR_000225) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Proper citation: FastQ Screen (RRID:SCR_000141) Copy   

•   Source: SciCrunch Registry

http://www.tcd.ie/

A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level.

Proper citation: Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) Copy   

•   Source: SciCrunch Registry

http://www.ufl.edu/

Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences.

Proper citation: University of Florida; Florida; USA (RRID:SCR_000145) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ms-spectre/

Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.

Proper citation: MS-Spectre (RRID:SCR_000266) Copy   

•   Source: SciCrunch Registry

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

Software that establishes a bridge between GEO and BioConductor.

Proper citation: GEOquery (RRID:SCR_000146) Copy   

•   Source: SciCrunch Registry

https://www.gov.pl/web/science

Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research.

Proper citation: Polish Ministry of Science and Higher Education (RRID:SCR_000251) Copy   

•   Source: SciCrunch Registry

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

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

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

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://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://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