Tools   Select Another Resource Report Type

http://mvaspike.gforge.inria.fr/

Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats.

Proper citation: Mvaspike (RRID:SCR_014760) Copy   

•   Source: SciCrunch Registry

http://www.eyesopen.com/oedocking

Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses.

Proper citation: FRED - Fast exhaustive docking (RRID:SCR_014885) Copy   

•   Source: SciCrunch Registry

https://cactus.nci.nih.gov/ncidb2.2/

Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group.

Proper citation: Open National Cancer Institute Database (RRID:SCR_014886) Copy   

•   Source: SciCrunch Registry

http://www.jadesantiago.com/Electrophysiology/IonChannelLab/

Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista.

Proper citation: IonChannelLab (RRID:SCR_014762) Copy   

•   Source: SciCrunch Registry

http://libroadrunner.org/

Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.

Proper citation: libRoadRunner (RRID:SCR_014763) Copy   

•   Source: SciCrunch Registry

http://www.lji.org

Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation.

Proper citation: La Jolla Institute for Immunology (RRID:SCR_014845) Copy   

•   Source: SciCrunch Registry

http://www.essex.ac.uk/

A public research university in Colchester, Essex, England. The institution has degree programs that span the humanities, social sciences, and health.

Proper citation: University of Essex; England; United Kingdom (RRID:SCR_014725) Copy   

•   Source: SciCrunch Registry

https://imdevsoftware.wordpress.com/tutorials/

A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals.

Proper citation: TeachingDemos (RRID:SCR_014689) Copy   

•   Source: SciCrunch Registry

http://cxidb.org

Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide.

Proper citation: Coherent X-Ray Imaging Data Bank (CXIDB) (RRID:SCR_014722) Copy   

•   Source: SciCrunch Registry

https://archive.data.jhu.edu/

Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.

Proper citation: Johns Hopkins Research Data Repository (RRID:SCR_014728) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

http://computation.llnl.gov/projects/sundials/cvode

Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CVODE (RRID:SCR_014696) Copy   

•   Source: SciCrunch Registry

http://ibrain.nuaa.edu.cn/

Brain research group affiliated with the Nanjing University of Aeronautics and Astronautics (NUAA) in China. The main research interests of iBRAIN include developing methods in machine learning, data mining, neural computation, and related areas for decoding brain functions or recognizing brain disease. Research related code and datasets can be found on the main site.

Proper citation: iBRAIN (RRID:SCR_014691) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/SparseTracer

Software used to automatically trace single neurons. It supports VTK 3D visualization.

Proper citation: SparseTracer (RRID:SCR_014736) Copy   

•   Source: SciCrunch Registry

http://www.splitstree.org/

Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SplitsTree (RRID:SCR_014734) Copy   

•   Source: SciCrunch Registry

http://www.analog-electronics.eu/slicap/slicap.html

A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.

Proper citation: SLiCAP (RRID:SCR_014742) Copy   

•   Source: SciCrunch Registry

http://www.egr.msu.edu/~wierzba/index_Page533.htm

Analog circuit analyzer and approximator used as a pre-processor to find design formulas or as a post-processor to approximate design formulas. The program performs the .AC analysis in SPICE symbolically with optional numeric evaluation and user selected threshold approximation.

Proper citation: Symbolic SPICE (RRID:SCR_014743) Copy   

•   Source: SciCrunch Registry

http://server.molgenrug.nl/index.php/prokaryote-promoters

A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run.

Proper citation: PePPER Prokaryote Promoter Prediction (RRID:SCR_014740) Copy   

•   Source: SciCrunch Registry

https://www.swarthmore.edu/NatSci/echeeve1/Ref/mna/MNA6.html

Software toolbox for deriving and solving circuit equations symbolically in MATLAB.

Proper citation: SCAM (RRID:SCR_014741) Copy   

•   Source: SciCrunch Registry

http://www.adaptivebiotech.com

Commercial organization which combines high-throughput sequencing and bioinformatics to profile T-cell and B-cell receptors.

Proper citation: Adaptive Biotechnologies (RRID:SCR_014709) Copy   

•   Source: SciCrunch Registry