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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Mar 18, 2019)

Physical Resource or Software Tool Software

16,472 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
QuidelResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_006146(Quidel, RRID:SCR_006146)Last checked upnlx_152444
HiTECResource, software resourceAccurate error correction in high-throughput sequencing data.SCR_011826(HiTEC, RRID:SCR_011826)listed by: OMICtoolsLast checked upOMICS_01105
Dhruv Dental Stem Cell BankResource, biomaterial supply resource, material resource, tissue bankNot yet vetted by NIF curatorSCR_010744(Dhruv Dental Stem Cell Bank, RRID:SCR_010744)Last checked upnlx_98186
SIMPLEXResource, software resourceCloud-enabled pipeline for the comprehensive analysis of exome sequencing data.SCR_010807(SIMPLEX, RRID:SCR_010807)listed by: OMICtoolsLast checked upOMICS_00294
nmrMLResource, narrative resource, interchange format, markup language, standard specification, data or information resourceAn open mark-up language for NMR data.nuclear magnetic resonanceSCR_000467(nmrML, RRID:SCR_000467)Last checked upnlx_157309
Latvia BiobankResource, biomaterial supply resource, material resourceA tissue donation bank based in Latvia. This resource is in Latvian.tissue, bank, biobank, latvia, nationalSCR_000927(Latvia Biobank, RRID:SCR_000927)Last checked upnlx_55758
SHOREResource, software resourceA mapping and analysis pipeline for short read data produced on the Illumina platform.SCR_011863(SHORE, RRID:SCR_011863)listed by: OMICtoolsLast checked upOMICS_01136
Nothing's ShockingResource, narrative resource, data or information resourceA neuroscience blog written by Noah Gray.neuroscience, blog, writing, article, noah graySCR_000932(Nothing's Shocking, RRID:SCR_000932)Last checked downnlx_80372
GAMESResource, software resourceSoftware that identifies and annotates mutations in next-generation sequencing projects.SCR_010762(GAMES, RRID:SCR_010762)listed by: OMICtoolsLast checked downOMICS_00060
York University; Ontario; CanadaResource, university, institutionSCR_006670(York University; Ontario; Canada, RRID:SCR_006670)Last checked downnlx_18471
Epoch Clinical Trial OntologyResource, ontology, data or information resource, controlled vocabularyOntology of clinical trial terminology.owlSCR_000366(Epoch Clinical Trial Ontology, RRID:SCR_000366)listed by: BioPortalLast checked upnlx_157400
SyapseResource, software resource, service resource, commercial organizationA platform and application suite for bringing together omics and clinical data.medicine, molecular profiling, omics, clinicalSCR_012023(Syapse, RRID:SCR_012023)listed by: OMICtoolsLast checked upOMICS_02092
hivebenchResource, software resource, commercial organizationA commercial software laboratory notebook.protocol sharing toolSCR_000915(hivebench, RRID:SCR_000915)Last checked upnlx_158032
British Heart FoundationResource, regional funding resource, group, funding resourceBritish charity and fundraiser for cardiovascular research.cardiovascular research, coronary heart disease, fundraisingSCR_002905(British Heart Foundation, RRID:SCR_002905)Last checked upnlx_82345
DiacloneResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_013526(Diaclone, RRID:SCR_013526)Last checked upnlx_152344
bam2wigResource, software resource, software applicationA script to convert Bam alignments into a wig representation file.SCR_015697(bam2wig, RRID:SCR_015697)submitted by: Resource Identification PortalLast checked down
4PeaksResource, software resource, software applicationSoftware application for viewing and editing sequence trace files.mac os x, sequence, trace fileSCR_000015(4Peaks, RRID:SCR_000015)listed by: OMICtoolsLast checked upOMICS_01015
University of Bristol; Bristol; United KingdomResource, university, institutionSCR_011613(University of Bristol; Bristol; United Kingdom, RRID:SCR_011613)related to: PharmaCog, PhenoSpDLast checked upnlx_14701
Common naming projectResource, portal, community building portal, data or information resourceScience Commons, OBO Foundry, and several other groups working with biological information on the Semantic Web have initiated an effort to establish shared community-maintained URIs for important data integration points such as life sciences database records (example: the record in the Entrez Gene database that has GeneID 1003064). We are attempting to determine the right technical and organizational recipe that will lead to the uptake of these URIs by a as many RDF-using bioinformatics projects as possible. Were this to be a success, one would be able to mash up information from multiple sources in a wide variety of ways, using the shared URIs to forge links between pieces. Information could be extracted from one source for inclusion in another; information could be combined in SPARQL queries using multiple FROM clauses; extractions from several triple stores could be combined to create a new one. Without shared URIs, this kind of integration would still be possible, but it would be significantly more difficult as it would require some kind of plumbing or mapping to get the two result sets to link up. Requirements We are limiting our concern for now to URIs for records in databases mentioned in external links from the Gene Ontology (GO), such as those from Enzyme or Pfam, with possible extension to other databases such as those in the LSRN (Life Science Resource Name) registry. The URIs we propose are meant to serve the community of Semantic Web-enabled bioinformatics projects that need URIs that refer to or denote database records. We identify the following requirements for URIs to serve a community and to be shared among Semantic Web projects: 1. It must be clearly stated what the intended referent of each URI is supposed to be, i.e. that the URI denotes some particular record from some particular database. 2. Information about the URI and its referent, including such a statement, must be made available, and in order to leverage existing protocol stacks, it must be obtainable via HTTP. (We'll call such information URI documentation.) 3. URI documentation must be provided in RDF. 4. Provision of URI documentation must be an ongoing concern. The ability to provide it may have to outlive the original database or the database's creator. 5. The provider of the URI documentation must be responsive to community needs, such as the need to have mistakes fixed in a timely manner. 6. URI documentation must be open so that it can be replicated and reused. Control of shared URIs should be in the hands of those who depend on them. This is the best way to ensure that the URIs serve the community in the ways listed above. Overall design The idea is to manage a server, or a set of servers, that can deliver appropriate RDF documents for the shared URIs. An HTTP GET of a URI would retrieve not the database record itself, but rather one of these RDF documents (perhaps via a 303 redirect). The RDF document will include the following: 1. Documentation specifying what the URI denotes (URI documentation), including an rdf:type, the database that the record comes from, and the record's identifier or key within that database. 2. Links to the various encodings of the record provided by the data provider, e.g. XML, ASN, HTML for the NCBI databases and so on. Each of these encodings would in turn have its own URI naming that particular encoding of the record, the main URI being the name of the record without commitment as to encoding. 3. Links as appropriate to corresponding resources belonging to semantic web projects participating in the common naming scheme, e.g. 4. Links as appropriate to related external resources that build on the database record. For example, the RDF for PubMed record 15456405 could link out to the iHOP page for the article described by the PubMed record. 5. Other information related to the record that might be of use to a human reader or automated agent. External links can be represented rigorously in RDF, allowing programs that access the RDF to proceed deterministically not only to the various encodings but also to any of the various related resources. This might be accomplished by having a distinct property for each participating project, or in some other way. We do not generally expect the RDF to include any of the content of the database record, although there is no particular reason to rule this out (except in cases where license terms preclude it). science, commons, biological, bioinformatic, namingbioinformatic, biological, commons, naming, scienceSCR_000757(Common naming project, RRID:SCR_000757)Last checked downnif-0000-20972
GEArray Expression Analysis Suite 2.0Resource, software resourceTHIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos.SCR_000282(GEArray Expression Analysis Suite 2.0, RRID:SCR_000282)Last checked upnif-0000-30602
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