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Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.
Proper citation: Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) Copy
https://amp.pharm.mssm.edu/covid19/
Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.
Proper citation: COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) Copy
Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis.
Proper citation: astropy (RRID:SCR_018148) Copy
Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy
https://www.lungepigenome.org/
Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum.
Proper citation: Lung Genome Browser (RRID:SCR_019255) Copy
Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.
Proper citation: GlyGen (RRID:SCR_023438) Copy
http://www.ncbi.nlm.nih.gov/unigene
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.
Proper citation: UniGene (RRID:SCR_004405) Copy
Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent.
Proper citation: BioJava Project (RRID:SCR_007180) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities.
Proper citation: Duke University Medical Center Neuropsychiatric Imaging Research Laboratory (RRID:SCR_007124) Copy
https://commonfund.nih.gov/hmp/
NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.
Proper citation: Human Microbiome Project (RRID:SCR_012956) Copy
http://www.usadellab.org/cms/index.php?page=trimmomatic
Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
Proper citation: Trimmomatic (RRID:SCR_011848) Copy
https://sciex.com/products/software/lipidview-software
Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.
Proper citation: LipidView Software (RRID:SCR_017003) Copy
https://gitlab.com/KHanghoj/DamMet
Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
Proper citation: DamMet (RRID:SCR_016959) Copy
Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control.
Proper citation: stop-signal task resources (RRID:SCR_017137) Copy
https://hub.docker.com/r/mziemann/tallyup/
Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.
Proper citation: Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) Copy
http://cab.spbu.ru/software/rnaquast/
Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.
Proper citation: rnaQUAST (RRID:SCR_016994) Copy
https://github.com/ropenscilabs/datastorr
Software package for simple data retrieval and versioning.
Proper citation: datastorr (RRID:SCR_017040) Copy
https://openknowledgemaps.org/
Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge.
Proper citation: Open Knowledge Maps (RRID:SCR_016470) Copy
https://www.ncbi.nlm.nih.gov/genbank/wgs/
Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database.
Proper citation: Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) Copy
https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission.
Proper citation: tbl2asn (RRID:SCR_016636) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
