Tools   Select Another Resource Report Type

http://krebs.iab.keio.ac.jp/HERMIT1/app/NichoAnu/

Metabolic pathway map that collects metabolic data gathered from multiple public databases and organizes them in one central location.

Proper citation: Ultimate Rough Aggregation of Metabolic Map (RRID:SCR_014694) Copy   

•   Source: SciCrunch Registry

https://senselab.med.yale.edu/MicroCircuitDB/

A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity.

Proper citation: MicrocircuitDB (RRID:SCR_014577) Copy   

•   Source: SciCrunch Registry

https://repod.pon.edu.pl/#annotations:cE6FdKHvEeaGt1e4NLwMyg

An online platform for open source data/datasets created, collected or annotated for scientific research of all fields and disciplines. Registered users can share data relating to their research project and view data from other projects. Groups can combine datasets into collections associated with the group, in contrast to individual members of the group hosting their own data.

Proper citation: RepOD (RRID:SCR_014697) Copy   

•   Source: SciCrunch Registry

https://figshare.com/articles/phi_toolbox_zip/3203326

Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.

Proper citation: Phi Toolbox (RRID:SCR_015549) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

https://astrocyte.rnaseq.sofroniewlab.neurobio.ucla.edu

Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions.

Proper citation: Astrocyte Reactivity RNA-Seq Browser (RRID:SCR_015033) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH

Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.

Proper citation: Embassy-domsearch (RRID:SCR_016086) Copy   

•   Source: SciCrunch Registry

https://www.rapidnovor.com/resources/wild/

Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments.

Proper citation: WILD (RRID:SCR_016240) Copy   

•   Source: SciCrunch Registry

http://jcggdb.jp/rcmg/glycodb/Ms_ResultSearch

A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans.

Proper citation: Glycan Mass Spectral Database (GMDB) (RRID:SCR_014667) Copy   

•   Source: SciCrunch Registry

https://www.nist.gov/srd/nist-standard-reference-database-1a-v14

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Proper citation: Mass Spectral Library (RRID:SCR_014668) Copy   

•   Source: SciCrunch Registry

https://searchbreast.org/

Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis.

Proper citation: SEARCHBreast (RRID:SCR_014826) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/datasets2tools/

Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.

Proper citation: Datasets2Tools (RRID:SCR_016174) Copy   

•   Source: SciCrunch Registry

https://github.com/common-workflow-language/cwltool

Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.

Proper citation: cwltool (RRID:SCR_015528) Copy   

•   Source: SciCrunch Registry

https://github.com/keepersecond/Soma-Segmentation

Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results.

Proper citation: Soma-Segmentation (RRID:SCR_015649) Copy   

•   Source: SciCrunch Registry

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

Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates.

Proper citation: UManitoba - JHU Functionally Defined Human White Matter Atlas (RRID:SCR_015525) Copy   

•   Source: SciCrunch Registry

http://reefgenomics.org/

Database for marine genomics data. Users can access genomics datasets from various organisms as well as carry out BLAST and submit genomics information of their own. Data sets include coral, aiptasia, sponges, and sybiodinium.

Proper citation: Reefgenomics (RRID:SCR_015009) Copy   

•   Source: SciCrunch Registry

http://cts.fiehnlab.ucdavis.edu

A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services.

Proper citation: Chemical Translation Service (RRID:SCR_014681) Copy   

•   Source: SciCrunch Registry

http://mamit-trna.u-strasbg.fr/Summary.asp

Compilation of mammalian mitochondrial tRNA genes. Sequences are classified into families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains.

Proper citation: Mamit tRNA (RRID:SCR_015493) Copy   

•   Source: SciCrunch Registry

http://imlspenticton.uzh.ch:3838/CATALYSTLite/

Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package.

Proper citation: CATALYSTLite (RRID:SCR_017126) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

•   Source: SciCrunch Registry