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Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation.
Proper citation: ConnecTF (RRID:SCR_022577) Copy
https://github.com/Cai-Lab-at-University-of-Michigan/nTracer
Software tool as plug-in for ImageJ software. Used for tracing microscopic images.
Proper citation: nTracer (RRID:SCR_023032) Copy
https://github.com/compbiolabucf/APA-Scan
Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.
Proper citation: APA-Scan (RRID:SCR_022974) Copy
Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.
Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy
Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets.
Proper citation: Kojak (RRID:SCR_021028) Copy
Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.
Proper citation: TargetScan (RRID:SCR_010845) Copy
https://midasnetwork.us/covid-19/
Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases.
Proper citation: Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) Copy
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
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
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
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
https://github.com/KarrLab/de_sim
Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.
Proper citation: DE-Sim (RRID:SCR_018770) Copy
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
http://sift.bii.a-star.edu.sg/
Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.
Proper citation: SIFT (RRID:SCR_012813) Copy
http://www.ccg.unam.mx/tfmodeller
Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs.
Proper citation: TFmodeller (RRID:SCR_015715) Copy
http://amp.pharm.mssm.edu/gen3va/
Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.
Proper citation: GEN3VA (RRID:SCR_015682) Copy
http://amp.pharm.mssm.edu/CREEDS/
Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.
Proper citation: CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) Copy
Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.
Proper citation: NeuroExpresso (RRID:SCR_015724) Copy
https://www.rosettacommons.org/home
Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
Proper citation: Rosetta (RRID:SCR_015701) Copy
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
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