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http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry

http://iupred.enzim.hu/

A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence.

Proper citation: IUPRED (RRID:SCR_014632) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/IQLAAEGABSFAKJMAUH

Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Proteome Discoverer (RRID:SCR_014477) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

http://www.biochem.mpg.de/5111795/maxquant

A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.

Proper citation: MaxQuant (RRID:SCR_014485) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

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

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET

Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces.

Proper citation: Brain Extraction Tool (RRID:SCR_014586) Copy   

•   Source: SciCrunch Registry

http://www.qsrinternational.com/nvivo-product

Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed.

Proper citation: NVivo (RRID:SCR_014802) Copy   

•   Source: SciCrunch Registry

http://paup.sc.fsu.edu

Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis.

Proper citation: PAUP (RRID:SCR_014931) Copy   

•   Source: SciCrunch Registry

https://www.mathworks.com/products/simulink/

Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems.

Proper citation: Simulink (RRID:SCR_014744) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry

http://spider.science.strath.ac.uk/sipbs/software_ses.htm

Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection.

Proper citation: WinWCP (RRID:SCR_014713) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/ligprep

Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.

Proper citation: Ligprep (RRID:SCR_016746) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/epik

Software program for pKa prediction and protonation state generation for drug like molecules.

Proper citation: Epik (RRID:SCR_016745) Copy   

•   Source: SciCrunch Registry

https://networkx.github.io/

Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Proper citation: NetworkX (RRID:SCR_016864) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/BRASS

Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.

Proper citation: BRASS (RRID:SCR_017091) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://www.microrna.org

Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: microRNA.org (RRID:SCR_006997) Copy   

•   Source: SciCrunch Registry

http://www.rms.org.uk/

It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs.

Proper citation: RMS (RRID:SCR_007415) Copy   

•   Source: SciCrunch Registry