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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

http://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) Copy   

•   Source: SciCrunch Registry

http://figshare.com/

Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.

Proper citation: FigShare (RRID:SCR_004328) Copy   

•   Source: SciCrunch Registry

http://eupathdb.org/eupathdb/

EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.

Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy   

•   Source: SciCrunch Registry

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

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://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=27

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available.

Proper citation: ChromasPro (RRID:SCR_000229) 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