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http://www.nitrc.org/projects/peak_nii/

Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command.

Proper citation: peak nii (RRID:SCR_002572) Copy   

•   Source: SciCrunch Registry

http://www.wolframalpha.com/

Wolfram Alpha is a computational knowledge engine that to make all systematic knowledge computable. Although, this is not a specific neuroscience related resource, the computational and math element will be helpful. Wolfram Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. It aims to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. It's goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries. Wolfram Alpha aims to also bring expert-level knowledge and capabilities to the broadest possible range of peoplespanning all professions and education levels. It's goal is to accept completely free-form input, and to serve as a knowledge engine that generates powerful results and presents them with maximum clarity. Lastly, Wolfram Alpha is an ambitious, long-term intellectual endeavor that it intends to deliver increasing capabilities over the years and decades to come. With a world-class team and participation from top outside experts in countless fields, it's goal is to create something that will stand as a major milestone of 21st century intellectual achievement. As of now, Wolfram Alpha contains 10+ trillion pieces of data, 50,000+ types of algorithms and models, and linguistic capabilities for 1000+ domains. Built with Mathematicawhich is itself the result of more than 20 years of development at Wolfram ResearchWolfram Alpha's core code base now exceeds 5 million lines of symbolic Mathematica code. Running on supercomputer-class compute clusters, Wolfram Alpha makes extensive use of the latest generation of web and parallel computing technologies, including webMathematica and gridMathematica. Its knowledge base and capabilities already span a great many domains, and its underlying framework has the power and flexibility to support ready extension to essentially any domain that is based on systematic knowledge.

Proper citation: Wolfram Alpha Computational Knowledge Engine (RRID:SCR_002693) Copy   

•   Source: SciCrunch Registry

http://cbb.sjtu.edu.cn/~ccwei/pub/software/CTF/CTF.php

Conditional random field (CRF) based transcription factor binding site (TFBS) finding system. The underlying CRF model can integrate features of different sources.

Proper citation: CTF (RRID:SCR_002692) Copy   

•   Source: SciCrunch Registry

http://www.vaa3d.org

A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.

Proper citation: Vaa3D (RRID:SCR_002609) Copy   

•   Source: SciCrunch Registry

http://funsimmat.bioinf.mpi-inf.mpg.de

FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool

Proper citation: FunSimMat (RRID:SCR_002729) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry

http://www.tractor-mri.org.uk/

Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.

Proper citation: TractoR: Tractography with R (RRID:SCR_002602) Copy   

•   Source: SciCrunch Registry

http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

•   Source: SciCrunch Registry

http://www.rbwb.org/

The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.

Proper citation: Rodent Brain WorkBench (RRID:SCR_002727) Copy   

•   Source: SciCrunch Registry

http://www.turtleseg.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process.

Proper citation: TurtleSeg (RRID:SCR_002605) Copy   

•   Source: SciCrunch Registry

http://www.zbi.ee/fungal-genomesize/

Database for scientists interested in fungal genomics. Multiple species are included, and the database provides information on DNA C-values and genomic size. It also gives information derived from electrophoresis experiments and genome sequencing projects. The database accepts data submissions. We appreciate receiving published offprints, preprints, and personal communications providing C-value estimates for fungi.

Proper citation: Fungal C-values Database (RRID:SCR_002726) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Genbank/

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Proper citation: GenBank (RRID:SCR_002760) Copy   

•   Source: SciCrunch Registry

http://www.uams.edu/

Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care.

Proper citation: University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) Copy   

•   Source: SciCrunch Registry

http://cpc.cbi.pku.edu.cn/

A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input.

Proper citation: Coding Potential Calculator (RRID:SCR_002764) Copy   

•   Source: SciCrunch Registry

http://www.opendoar.org/

A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining.

Proper citation: OpenDOAR (RRID:SCR_002641) Copy   

•   Source: SciCrunch Registry

http://www.gabipd.org/

Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research.
GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated.
* GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload.

Proper citation: Gabi Primary Database (RRID:SCR_002755) Copy   

•   Source: SciCrunch Registry

http://jcb-dataviewer.rupress.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

Proper citation: JCB DataViewer (RRID:SCR_002633) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/DSS.html

Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Proper citation: DSS (RRID:SCR_002754) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pirs/

Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.

Proper citation: pIRS (RRID:SCR_002519) Copy   

•   Source: SciCrunch Registry

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

•   Source: SciCrunch Registry