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http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://www.fei.com/software/amira-3d-for-life-sciences/

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

Proper citation: Advanced 3D Visualization and Volume Modeling (RRID:SCR_007353) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry

http://www.mitre.org/news/digest/archives/2002/neuroinformatics.html

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

Proper citation: MITRE Neuroinformatics (RRID:SCR_006508) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.

Proper citation: eQTL Visualization Tool (RRID:SCR_013413) Copy   

•   Source: SciCrunch Registry

http://www.hedtags.org/

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

Proper citation: HED Tags (RRID:SCR_014074) Copy   

•   Source: SciCrunch Registry

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.

Proper citation: Skyline (RRID:SCR_014080) Copy   

•   Source: SciCrunch Registry

http://www.originlab.com/index.aspx?go=PRODUCTS/Origin

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.

Proper citation: Origin (RRID:SCR_014212) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/tred

Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated.

Proper citation: Transcriptional Regulatory Element Database (RRID:SCR_005661) Copy   

•   Source: SciCrunch Registry

http://snpselector.duhs.duke.edu/hqsnp36.html

This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP. There are four kinds of SNP search you can do: * Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.) * Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc. * Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene. * Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions. A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).

Proper citation: High Quality SNP Database (RRID:SCR_007230) Copy   

•   Source: SciCrunch Registry

http://cmckb.cellmigration.org

It is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium.

Proper citation: CMKB (RRID:SCR_007229) Copy   

•   Source: SciCrunch Registry

http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

•   Source: SciCrunch Registry

https://leger2.helmholtz-hzi.de/cgi-bin/expLeger.pl

Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.

Proper citation: LEGER: the post-genome Database for Listeria Research (RRID:SCR_007760) Copy   

•   Source: SciCrunch Registry

http://www.genepath.org/

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.

Proper citation: GenePath (RRID:SCR_007974) Copy   

•   Source: SciCrunch Registry

https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry

http://www.type2diabetesgenetics.org/

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy   

•   Source: SciCrunch Registry

http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

•   Source: SciCrunch Registry

https://brainiak.org

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy   

•   Source: SciCrunch Registry