Tools   Select Another Resource Report Type

http://www.embl.de/

Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.

Proper citation: European Molecular Biology Laboratory (RRID:SCR_004473) Copy   

•   Source: SciCrunch Registry

https://www.fieldtriptoolbox.org

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

Proper citation: FieldTrip (RRID:SCR_004849) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

Proper citation: NCBI BLAST (RRID:SCR_004870) Copy   

•   Source: SciCrunch Registry

http://alt.kompetenznetz-parkinson.de/englisch/englisch.html

A medical network comprised of university clinics, special clinics, and special practices working together to collect data, gene samples, and execute clinical trials in order to bring about diagnoses and therapy methods. Research projects are done in cure research, diagnostic and therapeutic research. The care network includes university clinics, town clinics, special clinics for Parkinson's disease, specialists, and general practitioners.

Proper citation: Competence Network on Parkinson's Disease (RRID:SCR_005013) Copy   

•   Source: SciCrunch Registry

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

Proper citation: miRDeep (RRID:SCR_010829) Copy   

•   Source: SciCrunch Registry

http://www-01.ibm.com/software/uk/analytics/spss/

Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago.

Proper citation: SPSS (RRID:SCR_002865) Copy   

•   Source: SciCrunch Registry

http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) Copy   

•   Source: SciCrunch Registry

http://platform.visiome.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.

Proper citation: Visiome Platform (RRID:SCR_003049) Copy   

•   Source: SciCrunch Registry

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://brainproducts.com/productdetails.php?id=17

Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy   

•   Source: SciCrunch Registry

http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry

http://www.bzip.org/

A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.

Proper citation: bzip2 (RRID:SCR_000376) Copy   

•   Source: SciCrunch Registry

http://medicaldata.wikia.com/wiki/Main_Page

Portal serves as resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data.

Proper citation: Quality of Medical Data (RRID:SCR_000520) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://www.africacentre.ac.za/Biobank/tabid/460/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

Proper citation: Africa Centre Biobank (RRID:SCR_000638) Copy   

•   Source: SciCrunch Registry

http://www.isrec.isb-sib.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).

Proper citation: Computational Cancer Genomics Group (RRID:SCR_000772) Copy   

•   Source: SciCrunch Registry