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https://www.ibm.com/products/spss-statistics

Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.

Proper citation: IBM SPSS Statistics (RRID:SCR_016479) Copy   

•   Source: SciCrunch Registry

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry

https://github.com/jtamames/SqueezeMeta

Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.

Proper citation: SqueezeMeta (RRID:SCR_021821) Copy   

•   Source: SciCrunch Registry

http://computproteomics.bmb.sdu.dk:8192/app/PolySTest

Web service for statistical testing, data browsing and interactive visualization. Contains multiple statistical tests and new method to incorporate missing values. Robust statistical testing of proteomics data with missing values to improve detection of biologically relevant features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PolySTest (RRID:SCR_021942) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/BASiCS/

Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.

Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) Copy   

•   Source: SciCrunch Registry

https://omgenomics.com/circa/

Software tool used to plot circular plots and visualize genomic data along genomic locations.

Proper citation: Circa (RRID:SCR_021828) Copy   

•   Source: SciCrunch Registry

http://combo.dbe.unifi.it/medusa

Web server of multi draft based scaffolder.Exploits information obtained from set of genomes from related organisms to determine correct order and orientation of contigs.

Proper citation: MeDuSa (RRID:SCR_022058) Copy   

•   Source: SciCrunch Registry

https://proq3.bioinfo.se/

Improved model quality assessments using Rosetta energy terms. Predictor combines training features from ProQRosCen, ProQRosFA and ProQ2.

Proper citation: ProQ3 (RRID:SCR_021880) Copy   

•   Source: SciCrunch Registry

https://www.mines.edu/

Public research university in Golden, Colorado, founded in 1874. School offers both undergraduate and graduate degrees in engineering, science, and mathematics, with focus on energy and environment.

Proper citation: Colorado School of Mines; Golden; Colorado (RRID:SCR_022054) Copy   

•   Source: SciCrunch Registry

https://prosa.services.came.sbg.ac.at/prosa.php

Interactive web service for recognition of errors in three dimensional structures of proteins.

Proper citation: ProSA web (RRID:SCR_021879) Copy   

•   Source: SciCrunch Registry

http://dunbrack.fccc.edu/pisces/

Software tool as protein sequence culling server. Used for culling sets of protein sequences from Protein Data Bank (PDB) by sequence identity and structural quality criteria. Can provide lists culled from entire PDB or from lists of PDB entries or chains provided by user.

Proper citation: PISCES (RRID:SCR_022181) Copy   

•   Source: SciCrunch Registry

http://cprc.rcm.upr.edu/?q=node/117

Facilitates supply of conventional and specific pathogen free nonhuman primates and biological samples. Priority is given to NIH-funded investigators in universities, NIH Intramural Program, and contractors working on behalf of researchers conducting experiments under NIH-funded programs. Non-NIH-funded investigators may still be considered depending on resource availability.To request for CPRC animals, authorized representative of institution will need to submit Animal Allocation Request form.

Proper citation: University of Puerto Rico Caribbean Primate Research Center (RRID:SCR_021920) Copy   

•   Source: SciCrunch Registry

http://biomine.cs.vcu.edu/servers/MFDp2/

Web tool for accurate prediction of disorder in proteins by fusion of disorder probabilities, content and profiles.

Proper citation: MFDp2 (RRID:SCR_021885) Copy   

•   Source: SciCrunch Registry

https://prdos.hgc.jp/cgi-bin/top.cgi

Web server to predict natively disordered regions of protein chain from its amino acid sequence. Returns disorder probability of each residue as prediction results.

Proper citation: PrDOS (RRID:SCR_021886) Copy   

•   Source: SciCrunch Registry

http://sysbio.rnet.missouri.edu/3Drefine/

Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis.

Proper citation: 3DRefine (RRID:SCR_021883) Copy   

•   Source: SciCrunch Registry

http://jspecies.ribohost.com/jspeciesws/#analyse

Web server for prokaryotic species circumscription based on pairwise genome comparison. Service for in silico calculating extent of identity between two genomes, parameter routinely used in process of polyphasic microbial species circumscription. Service measures average nucleotide identity.

Proper citation: JSpeciesWS (RRID:SCR_022059) Copy   

•   Source: SciCrunch Registry

https://www.trikinetics.com/Downloads/DAMSystem3%20Software%20Data%20Sheet.pdf

Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System.

Proper citation: TriKinetics DAMSystem3 Software (RRID:SCR_021809) Copy   

•   Source: SciCrunch Registry

https://cpndb.ca/

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy   

•   Source: SciCrunch Registry

http://www.theseed.org/wiki/Home_of_the_SEED

The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org

Proper citation: SEED (RRID:SCR_002129) Copy   

•   Source: SciCrunch Registry

http://arrowsmith.psych.uic.edu/arrowsmith_uic/

Portal for documenting the Arrowsmith project and developing text mining tools for scientific, and specifically neuroscience, literature. It also contains a search functions that identifies similar concepts between two articles.

Proper citation: Arrowsmith (RRID:SCR_002523) Copy   

•   Source: SciCrunch Registry