Tools   Select Another Resource Report Type

http://ls-snp.icm.jhu.edu/ls-snp-pdb/

A web tool for genome-wide annotation of human SNPs.

Proper citation: LS-SNP/PDB (RRID:SCR_010774) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/PlantTFcat/

A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PlantTFcat (RRID:SCR_010898) Copy   

•   Source: SciCrunch Registry

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

A flexible tool for visualizing and analyzing your two-colour microarray slides.

Proper citation: ArrayPipe (RRID:SCR_010934) Copy   

•   Source: SciCrunch Registry

http://model.nmr.ru/preddimer/

Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices.

Proper citation: PREDDIMER (RRID:SCR_011963) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/phyml/

Web phylogeny server based on the maximum-likelihood principle.

Proper citation: PhyML (RRID:SCR_014629) Copy   

•   Source: SciCrunch Registry

http://multiqc.info/

Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.

Proper citation: MultiQC (RRID:SCR_014982) 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

https://github.com/TGAC/RAMPART

Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.

Proper citation: Rampart (RRID:SCR_016742) Copy   

•   Source: SciCrunch Registry

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) 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://steps.sourceforge.net/STEPS/default.php

STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.

Proper citation: STEPS (RRID:SCR_008742) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARS (RRID:SCR_009123) Copy   

•   Source: SciCrunch Registry

https://www.integromics.com/omicsoffice-for-ngs/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy   

•   Source: SciCrunch Registry

http://www.bioinfor.com/zoom/general/overview.html

Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

Proper citation: ZOOM (RRID:SCR_002175) Copy   

•   Source: SciCrunch Registry

http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html

VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, users can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. * Search homologous protein families from particular virus families * Links to complete genome sequence: Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIDA (RRID:SCR_007111) Copy   

•   Source: SciCrunch Registry

http://www.neuromatic.thinkrandom.com/

NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC

Proper citation: NeuroMatic (RRID:SCR_004186) Copy   

•   Source: SciCrunch Registry

http://ratmine.mcw.edu/ratmine/begin.do

RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites.

Proper citation: RatMine (RRID:SCR_004190) Copy   

•   Source: SciCrunch Registry

http://biorxiv.org/

A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.

Proper citation: bioRxiv (RRID:SCR_003933) Copy   

•   Source: SciCrunch Registry

http://git-scm.com/

A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.

Proper citation: Git (RRID:SCR_003932) Copy   

•   Source: SciCrunch Registry

https://github.com/alyssafrazee/derfinder

R package for differential expression analysis of RNA-seq data.

Proper citation: DER Finder (RRID:SCR_004250) Copy   

•   Source: SciCrunch Registry