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http://www.roslin.ed.ac.uk/about-roslin/

The world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio.

Proper citation: Roslin Wellcome Trust Tick Cell Biobank (RRID:SCR_004228) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

Proper citation: ARNIE (RRID:SCR_000514) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/biolexicon/

A large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources.

Proper citation: BioLexicon (RRID:SCR_000589) Copy   

•   Source: SciCrunch Registry

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry

http://www.hipsci.org/

A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.

Proper citation: HipSci (RRID:SCR_003909) Copy   

•   Source: SciCrunch Registry

https://github.com/c-zhou/yahs

Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.

Proper citation: YaHS (RRID:SCR_022965) Copy   

•   Source: SciCrunch Registry

http://labs.europepmc.org/evf

A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.

Proper citation: EvidenceFinder (RRID:SCR_013764) Copy   

•   Source: SciCrunch Registry

http://tiger.bsc.es

Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.

Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/lohhla

Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data.

Proper citation: LOHHLA (RRID:SCR_023690) Copy   

•   Source: SciCrunch Registry

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

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

http://www.cancerrxgene.org/

A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs.

Proper citation: Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) Copy   

•   Source: SciCrunch Registry

http://www.sherpa.ac.uk/romeo/index.php?la=en&fIDnum=/&mode=simple

A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit.

Proper citation: SHERPA RoMEO (RRID:SCR_013815) Copy   

•   Source: SciCrunch Registry

http://old.genedb.org/genedb/pombe/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE documented June 6, 2013 Database of all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824, has been sequenced and annotated. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

Proper citation: GeneDB Spombe (RRID:SCR_010639) Copy   

•   Source: SciCrunch Registry

http://caps.ncbs.res.in/imotdb/

Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members.

Proper citation: Database of Spatially Interacting Motifs in Proteins (RRID:SCR_007735) Copy   

•   Source: SciCrunch Registry

https://vertebrate.genenames.org/

Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.

Proper citation: VGNC (RRID:SCR_017514) Copy   

•   Source: SciCrunch Registry

http://www.alspac.bris.ac.uk

A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.

Proper citation: ALSPAC (RRID:SCR_007260) Copy   

•   Source: SciCrunch Registry

http://crosslinkviewer.org/

Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.

Proper citation: xiNET (RRID:SCR_021010) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/ploras#annotations:QXuC2C7REeaxtw-aEPo07Q

A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others.

Proper citation: Predicting Language Outcome and Recovery After Stroke (PLORAS) (RRID:SCR_014498) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry