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http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://modbase.compbio.ucsf.edu/foxs/

Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data.

Proper citation: FoXS (RRID:SCR_017269) Copy   

•   Source: SciCrunch Registry

https://www.beast2.org/

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

Proper citation: BEAST2 (RRID:SCR_017307) Copy   

•   Source: SciCrunch Registry

https://amp.pharm.mssm.edu/geneshot/

Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.

Proper citation: Geneshot (RRID:SCR_017582) Copy   

•   Source: SciCrunch Registry

http://neuroproteomics.scs.illinois.edu/microMS.htm

Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing.

Proper citation: microMS (RRID:SCR_017443) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://evcouplings.org/

Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.

Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) Copy   

•   Source: SciCrunch Registry

https://www.bcforms.org

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

Proper citation: BcForms (RRID:SCR_018654) Copy   

•   Source: SciCrunch Registry

https://www.datanator.info

Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.

Proper citation: Datanator (RRID:SCR_018651) Copy   

•   Source: SciCrunch Registry

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.

Proper citation: RiboTaper (RRID:SCR_018880) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/EDTSurf/

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

Proper citation: Edtsurf (RRID:SCR_016083) Copy   

•   Source: SciCrunch Registry

https://github.com/sorgerlab/ashlar

Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.

Proper citation: ASHLAR (RRID:SCR_016266) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry

https://www.proteinmetrics.com/products/byonic/

Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.

Proper citation: PMI-Byonic (RRID:SCR_016735) Copy   

•   Source: SciCrunch Registry

https://github.com/hakyimlab/PrediXcan

Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.

Proper citation: PrediXcan (RRID:SCR_016739) Copy   

•   Source: SciCrunch Registry

http://rlbl.chem.upenn.edu

Biomedical technology research center and training resource that develops time-resolved laser technologies and instrumentation, with a focus on 2-D IR spectroscopy. The technologies enable atomic-level measurements of the fastest steps in biological processes to elucidate structure and dynamics in biological macromolecules, assemblies and cells. The Center makes most of its instrumentation available for service research projects to outside users nation-wide.

Proper citation: Ultrafast Optical Processes Laboratory (RRID:SCR_006582) Copy   

•   Source: SciCrunch Registry