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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: Jul 13, 2019)

Physical Resource or Software Tool Software

16,652 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
TransGenicResource, reagent supplier, material resource, antibody supplierA commercial antibody supplier and knockout mice producer.commercial organization, antibody supplier, knockout mouseSCR_000001(TransGenic, RRID:SCR_000001)Last checked upnlx_152482
TabletResource, software resourceA lightweight, high-performance graphical viewer for next generation sequence assemblies and generation sequence, assembly, alignmentSCR_000017(Tablet, RRID:SCR_000017)James Hutton Institute; Scotland; United Kingdom listed by: OMICtoolsPMID:22445902Last checked upOMICS_00896
GenomicRangesResource, software resourceSoftware package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.genomic intervalSCR_000025(GenomicRanges, RRID:SCR_000025)Bioconductor used by: riboWaltz, listed by: OMICtoolsLast checked upOMICS_01161
PatchmasterResource, software resource, data acquisition software, data processing software, commercial organization, software applicationMulti-channel data acquisition software.electrophysiologySCR_000034(Patchmaster, RRID:SCR_000034)Last checked upSciRes_000168
Batman-SeqResource, software resourceA fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.c++SCR_000048(Batman-Seq, RRID:SCR_000048)listed by: OMICtools, hosted by: SourceForgeLast checked upOMICS_00651
Academia.eduResource, portal, community building portal, data or information resourceSocial networking site for academic researchers that allows researchers to share papers, find people working in a field and see analytics on papers etcsocial networking, altmetrics, analytics, paper, research interest, job resourceSCR_000080(, RRID:SCR_000080)listed by: FORCE11Last checked upnlx_152526
StratMLResource, narrative resource, interchange format, markup language, standard specification, data or information resourceAn XML vocabulary and schema for strategic plans, designed to create a world wide web of intentions, stakeholders and results.xml, vocabulary, schema, annotation, strategic plan, strategySCR_000081(StratML, RRID:SCR_000081)listed by: FORCE11Last checked upnlx_152542
AbMining ToolBoxResource, software resourcePython scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).standalone software, illumina, roche, life technologies, pythonSCR_000090(AbMining ToolBox, RRID:SCR_000090)SourceForge listed by: OMICtoolsPMID:24423623Last checked upOMICS_04063
Google SitesResource, service resourceA free online service to easily create and share, sharing, authoring toolSCR_000112(Google Sites, RRID:SCR_000112)Last checked upnlx_157257
Project HaloResource, organization portal, portal, data or information resourceProject Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.project, tutor, research assistant, science, knowledge-base, semantic mediawiki, ontology, textbook, book, training material, digital book, data mining, biologySCR_000136(Project Halo, RRID:SCR_000136)Stanford Research Institute International Last checked downnlx_144483
Mind HacksResource, blog, narrative resource, book, data or information resourceMind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.neuroscience, psychology, brainSCR_000170(Mind Hacks, RRID:SCR_000170)used by: NIF Data Federation, Integrated BlogsLast checked downnlx_48997
Surflex-DockResource, software resourceA software program that screens large libraries of compounds including ligands, and their docking.ligand docking, library, compound, compound librarySCR_000196(Surflex-Dock, RRID:SCR_000196)listed by: OMICtoolsPMID:22569590Last checked upOMICS_01607
Duplicate reads removalResource, software resource, commercial organizationPlug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.pcr amplification, duplicate, readSCR_000231(Duplicate reads removal, RRID:SCR_000231)listed by: OMICtoolsLast checked downOMICS_02101
RNAmotifsResource, software resourceSoftware that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.rna, motifSCR_000263(RNAmotifs, RRID:SCR_000263)Bitbucket listed by: OMICtoolsLast checked downOMICS_02287
RNASeqReadSimulatorResource, software resourceA software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.rna-seq, command lineSCR_000270(RNASeqReadSimulator, RRID:SCR_000270)listed by: OMICtoolsLast checked upOMICS_01964
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
Proteomics and Human Proteome: From Bench to BedsideResource, video resource, data or information resourceThis website contains lecture videos from the events and discussions of the SEProt congress meeting, the theme of which is Human proteome. From Bench to Bedside. Sponsors: These videos are supported by the University of Navarra.congress, human, lecture, proteomeSCR_000285(Proteomics and Human Proteome: From Bench to Bedside, RRID:SCR_000285)Last checked upnif-0000-10402
IndeedResource, job resourceA database of job listingsemployment, careerSCR_000292(Indeed, RRID:SCR_000292)related to: Integrated Jobs, used by: NIF Data FederationLast checked upnlx_144165
University of Zaragoza; Zaragoza; SpainResource, undergraduate program resource, graduate program resource, degree granting program, training resourceAn undergraduate and postgraduate university which is located in Zaragoza, Spain.zaragoza, university, undergraduate, postgraduateSCR_000341(University of Zaragoza; Zaragoza; Spain, RRID:SCR_000341)Last checked upnlx_144537
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
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