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SciCrunch: Registry

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

(last updated: Apr 21, 2018)

Physical Resource or Software Tool Software

15,804 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Cell SciencesResource, commercial organization, reagent supplier, material resource, antibody supplierAn Antibody supplierSCR_004502(Cell Sciences, RRID:SCR_004502)Last checked upnlx_152329
Innovation NorwayResource, government granting agencySCR_011298(Innovation Norway, RRID:SCR_011298)Last checked downnlx_156799
ScyTek LaboratoriesResource, commercial organization, reagent supplier, material resource, antibody supplierAn Antibody supplierSCR_005919(ScyTek Laboratories, RRID:SCR_005919)Last checked upnlx_152455
List BiologicalResource, commercial organization, reagent supplier, material resource, antibody supplierAn Antibody supplierSCR_013406(List Biological, RRID:SCR_013406)Last checked upnlx_152401
QDMRResource, software resourceSoftware that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.SCR_007162(QDMR, RRID:SCR_007162)listed by: OMICtoolsLast checked upOMICS_00623
ECM BiosciencesResource, commercial organization, reagent supplier, material resource, antibody supplierAn Antibody supplierSCR_004099(ECM Biosciences, RRID:SCR_004099)Last checked upnlx_152351
EurofungbaseResource, knowledge environmentThe Eurofung project is a Coordination Action with the aim of developing a strategy to build up and maintain an integrated, sustainable European genomic database required for innovative genomics research of filamentous fungal model organisms of interest. This database will become a crystallization point for related systems and then could be integrated and conserved in a central European genomic database. The consortium counts 32 member laboratories, three of which have partner status. A Fungal Industrial Platform (FIP) of 13 members is also associated with the project. The project focuses on several filamentous fungi for different reasons. Aspergillus nidulans has a long record of use as a fungal model organism. Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum are important cell factories used for the production of enzymes and metabolites including compounds such as Beta-lactams with benefits to human health. The human pathogen Aspergillus fumigatus serves not only as a model pathogen, but becomes more and more a serious threat to human health. The project contributes to create the conditions and facilities within Europe to widely apply all genomics technologies in filamentous fungal research. This will greatly expand our knowledge about filamentous fungi. This new genomics information will thus be beneficial to European biotechnology industries and help to improve the prevention and treatment of fungal disease. Expected results: The main results expected from this project are: - The contribution of the community to the manual annotation of important fungal genomes through annotation jamborees. - The realization of an integrated sustainable fungal genomic database through collaboration with bioinformatics centers and incorporation of the community data. - The realization of a fungal genomics knowledge base for the Eurofungbase community and the European fungal biotech industry through meetings, workshops and web-based information. - Intensified collaboration between the members of the network including the participating industries, thus strengthening the infrastructure for high quality fungal genomics research in Europe and furthermore determining joint research targets for the future. -Individualized training of a next generation of young scientists in fungal genomics and biotechnological research.SCR_007094(Eurofungbase, RRID:SCR_007094)European UnionLast checked downnlx_20616
FastDMAResource, software resourceA software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.SCR_010954(FastDMA, RRID:SCR_010954)listed by: OMICtoolsLast checked upOMICS_00794
EBARDenovoResource, software resourceHighly accurate de novo assembly of RNA-Seq with efficient chimera-detection.SCR_011890(EBARDenovo, RRID:SCR_011890)SourceForge listed by: OMICtoolsLast checked upOMICS_01317
Neurotechnology Industry OrganizationResource, organization portal, portal, data or information resourceThe Neurotechnology Industry Organization (NIO) is a non-profit trade association that represents companies involved in neuroscience (neuropharmaceuticals, cell-based therapeutics, neurodevices and neurodiagnostics), academic neuroscience research centers, and brain-illness advocacy groups across the United States and throughout the world. NIO was formed to provide a unified voice for the commerical neuroscience community. NIO advocates for its member organizations on a range of issues related to neurotechnology research and business development including favorable changes in the tax code, intellectual property issues, neuroethics, public policy, reimbursement and patient advocacy. Thank you for taking the time to read this brief introduction to the Neurotechnology Industry Organization (NIO), the recently formed trade association representing companies involved in neuroscience (drugs, devices and diagnostics), brain research centers, patient advocacy groups, and research foundations worldwide. NIO was founded in August 2006 and has attracted over 80 member organizations. NIO''s mission is to accelerate treatments and cures for brain and nervous system illnesses by: * Advocating neurotech''s position to government and regulatory officials * Promoting the industry''s progress and contributions to quality of life * Providing industry development services for our members NIO is spearheading several innovative programs that will benefit your company including: National Neurotechnology Initiative - a new $200M/year Federal initiative aimed at accelerating translational neuroscience innovation and improving the effectiveness of the FDA review process for neuroscience drugs, devices and diagnostics NIO/FDA private-public working group - an initiative to work collaboratively with the FDA to improve the efficiency of the evaluation process for neuroscience products and to increase communication and clarity during the regulatory process Partnering, investment and policy events - networking events with other members of the global commercial neuroscience community at events such as the annual public policy tour in March in Washington D.C. and the Neurotech investing and partnering conference in Spring National Visibility - NIO actively outreaches to global media outlets to encourage coverage of Neurotech that will foster great investor, policymaker and consumer interest. As a member of NIO you will enjoy the following benefits: * Influence in the industry''s overall development agenda * Access to key opinion leaders in Congress, regulatory agencies, media * Participation in FDA and CMS working groups, stakeholder meetings * Expanded networking at neurotech investing and partnering events throughout the year * Participation in neuroscience education awareness initiatives, public awareness campaigns * Industry leadership through participation in driving innovative legislation, new projects NIO''s programs increase awareness of commercial neuroscience products, reduce barriers to innovation, support industry growth and will benefit your company and industry. I hope that you will consider joining NIO in support of our mission to give the brain a voice..SCR_006556(Neurotechnology Industry Organization, RRID:SCR_006556)Last checked upnif-0000-00491
University of Rhode Island; Rhode Island; USAResource, university, institutionSCR_007656(University of Rhode Island; Rhode Island; USA, RRID:SCR_007656)Last checked upnlx_144351
Surgical Secondary EventsResource, ontology, data or information resource, controlled vocabularyMemorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events).owlSCR_007894(Surgical Secondary Events, RRID:SCR_007894)listed by: BioPortalLast checked upnlx_157598
Biodiversity OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology of biodiversity of INPAowlSCR_010204(Biodiversity Ontology, RRID:SCR_010204)listed by: BioPortalLast checked upnlx_157331
QUMAResource, software resourceYou can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.SCR_010907(QUMA, RRID:SCR_010907)listed by: OMICtoolsLast checked upOMICS_00588
Semantic DICOM OntologyResource, ontology, data or information resource, controlled vocabularyAn ontology for DICOM as used in the SeDI project.owlSCR_000309(Semantic DICOM Ontology, RRID:SCR_000309)listed by: BioPortalLast checked upnlx_157583
Bioinformatics ToolkitResource, software resource, software repositoryA platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.SCR_010277(Bioinformatics Toolkit, RRID:SCR_010277)Last checked upnlx_156936
CGHsegResource, software resourceR package dedicated to the analysis of CGH profiles using segmentation models.SCR_010922(CGHseg, RRID:SCR_010922)listed by: OMICtoolsLast checked upOMICS_00712
Texas Human BiologicsResource, production service resource, biomaterial supply resource, tissue bank, material service resource, service resource, material resourceNot yet vetted by NIF curatorSCR_010523(Texas Human Biologics, RRID:SCR_010523)Last checked upnlx_20452
SOAPdenovoResource, software resourceA short-read assembly method that can build a de novo draft assembly for the human-sized genomes.SCR_010752(SOAPdenovo, RRID:SCR_010752)listed by: OMICtoolsLast checked upOMICS_00031
WebScopeResource, image collection, data or information resourceExpansive collection of high-quality wholeslide imagesSCR_006355(WebScope, RRID:SCR_006355)Last checked upnlx_152089
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