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http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html
R software that detects enriched regions of ChIP-seq data sets jointly.
Proper citation: Jmosaics (RRID:SCR_001094) Copy
http://www.moleculardevices.com/products/software/pclamp.html
Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis.
Proper citation: pClamp (RRID:SCR_011323) Copy
https://github.com/najoshi/sabre
Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.
Proper citation: sabre (RRID:SCR_011843) Copy
http://www.bioconductor.org/packages/release/bioc/html/affy.html
Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.
Proper citation: affy (RRID:SCR_012835) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.
Proper citation: PlasmoDB (RRID:SCR_013331) Copy
http://www.cytobank.org/index.html
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
Proper citation: Cytobank (RRID:SCR_014043) Copy
Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.
Proper citation: ChEMBL (RRID:SCR_014042) Copy
http://scanimage.vidriotechnologies.com/
Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features.
Proper citation: ScanImage (RRID:SCR_014307) Copy
Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
Proper citation: UniProt (RRID:SCR_002380) Copy
Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.
Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy
http://www.nih.gov/science/brain/
Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.
Proper citation: BRAIN Initiative (RRID:SCR_006770) Copy
XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools.
Proper citation: XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) Copy
Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.
Proper citation: Data Biosphere (RRID:SCR_016154) Copy
http://reproducibility.stanford.edu/
Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.
Proper citation: Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) Copy
Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.
Proper citation: Inxight (RRID:SCR_016490) Copy
Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.
Proper citation: NeLS (RRID:SCR_016301) Copy
https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/
Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.
Proper citation: BASTA (RRID:SCR_017303) Copy
https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405
Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.
Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy
https://kona.nhgri.nih.gov/mnemiopsis/
Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis.
Proper citation: Mnemiopsis Genome Project Portal (RRID:SCR_018293) Copy
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