Tools   Select Another Resource Report Type

http://www.africacentre.ac.za/Default.aspx?tabid=69

Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.

Proper citation: Africa Centre for Health and Population Studies (RRID:SCR_008964) Copy   

•   Source: SciCrunch Registry

https://opentrials.net/

Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.

Proper citation: Open Trials (RRID:SCR_015570) Copy   

•   Source: SciCrunch Registry

http://mousebrain.org/

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

Proper citation: mousebrain.org (RRID:SCR_016999) Copy   

•   Source: SciCrunch Registry

http://geroprotectors.org

Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases.

Proper citation: GEROprotectors (RRID:SCR_016737) Copy   

•   Source: SciCrunch Registry

https://github.com/kjolley/BIGSdb

Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level.

Proper citation: BIGSdb (RRID:SCR_023551) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/huwjenkins/fragon

Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4.

Proper citation: fragon (RRID:SCR_019158) Copy   

•   Source: SciCrunch Registry

http://www.hdbr.org/

Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user''''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research.

Proper citation: Human Developmental Biology Resource (RRID:SCR_006326) Copy   

•   Source: SciCrunch Registry

http://merops.sanger.ac.uk/

An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

Proper citation: MEROPS (RRID:SCR_007777) Copy   

•   Source: SciCrunch Registry

http://www.mlst.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages.

Proper citation: MLST (RRID:SCR_010245) Copy   

•   Source: SciCrunch Registry

http://biorxiv.org/content/early/2013/11/27/000455

A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged.

Proper citation: Retinal wave repository (RRID:SCR_010462) Copy   

•   Source: SciCrunch Registry

https://github.com/muxingu/rnamut

Software package for robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Detects clinically important somatic mutations from RNA-seq data on relatively small gene panel (typically less than 100 genes).

Proper citation: RNAmut (RRID:SCR_026965) Copy   

•   Source: SciCrunch Registry

https://github.com/wershofe/TWOMBLI

Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix.

Proper citation: TWOMBLI (RRID:SCR_027217) Copy   

•   Source: SciCrunch Registry

https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.

Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy   

•   Source: SciCrunch Registry

https://www.openmicroscopy.org/site/products/bio-formats

Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.

Proper citation: Bio-Formats (RRID:SCR_000450) Copy   

•   Source: SciCrunch Registry

http://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) 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://tritrypdb.org/tritrypdb/

An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

Proper citation: TriTrypDB (RRID:SCR_007043) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/enzymes/

Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.

Proper citation: Enzyme Structures Database (RRID:SCR_007125) Copy   

•   Source: SciCrunch Registry