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http://www.biomart.org/biomart/martview/ddb9ce1ad275cde372c968d13fa11f5f

A web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services.

Proper citation: BioMart MartView (RRID:SCR_010714) Copy   

•   Source: SciCrunch Registry

http://europepmc.org/

Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.

Proper citation: Europe PubMed Central (RRID:SCR_005901) Copy   

•   Source: SciCrunch Registry

http://www.isrctn.com

A primary clinical trial registry which houses proposed, ongoing, and completed clinical research studies. An ISRCTN is a simple numeric system for the unique identification of randomized controlled trials worldwide. The registry provides content validation and curation and the unique identification number necessary for publication. Submitted studies range from cancer to urological diseases.

Proper citation: ISRCTN Registry (RRID:SCR_006087) Copy   

•   Source: SciCrunch Registry

http://www.pombase.org/

Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.

Proper citation: PomBase (RRID:SCR_006586) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ena/

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbsum

Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.

Proper citation: PDBsum (RRID:SCR_006511) Copy   

•   Source: SciCrunch Registry

http://embryoimaging.org/

Collection of high resolution images and movies of mouse and human embryos produced using high resolution episcopic microscopy (HREM). Each data set is a series of block-face images generated during sectioning through an entire embryo, typically cut at 2-3 micrometers. Datasets are organized by approximate developmental stage and each embryo has been assigned a specimen ID (SID) for identification. This is an ongoing project funded by the Wellcome Trust to provide comprehensive imaging of normal and mutant mouse embryos that will complement the standard anatomical texts and form the basis for systematic phenotyping. * Movies: A 3D reconstruction shows each embryo, and lower resolution movies created through each orthogonal plane enable you to quickly review the data set. * Image Stacks: In the stack viewer, you can step through the images in sequence, zoom in to see fine details and adjust the image contrast. * NEW: Embryo Comparison: Two image stacks can now be compared in the stack viewer.

Proper citation: Embryo Imaging (RRID:SCR_006329) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

•   Source: SciCrunch Registry

http://old.genedb.org/genedb/glossina/

As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.

Proper citation: GeneDB Gmorsitans (RRID:SCR_004310) Copy   

•   Source: SciCrunch Registry

https://github.com/xavierdidelot/clonalorigin

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

Proper citation: ClonalOrigin (RRID:SCR_016061) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/Roary/

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

Proper citation: Roary (RRID:SCR_018172) Copy   

•   Source: SciCrunch Registry

https://github.com/linnarsson-lab/cytograph

Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis.

Proper citation: Cytograph (RRID:SCR_023101) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@[email protected]

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

https://github.com/MetaCell/nwb-explorer

Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format.

Proper citation: NWB Explorer (RRID:SCR_021151) Copy   

•   Source: SciCrunch Registry

https://spikeinterface.readthedocs.io

Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs.

Proper citation: SpikeInterface (RRID:SCR_021150) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://github.com/alexlib/KymoButler-1

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

Proper citation: KymoButler (RRID:SCR_021717) Copy   

•   Source: SciCrunch Registry

https://shiny.cnsgenomics.com/mRnd/

Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach.

Proper citation: mRnd (RRID:SCR_022156) Copy   

•   Source: SciCrunch Registry