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DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.
Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy
https://alcazar.science.uu.nl/services/HADDOCK2.2/
Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface.
Proper citation: HADDOCK (RRID:SCR_019091) Copy
http://enterobase.warwick.ac.uk/
Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.
Proper citation: EnteroBase (RRID:SCR_019019) Copy
http://amphibian.hiroshima-u.ac.jp/english/ARC_HP_English_ver./english_page.html
Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis.
Proper citation: Hiroshima University Amphibian Research Center (RRID:SCR_019015) Copy
Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like.
Proper citation: PhyloPic (RRID:SCR_019139) Copy
https://github.com/medema-group/bigslice
Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data.
Proper citation: BiG-SLiCE (RRID:SCR_019130) Copy
https://www.openicpsr.org/openicpsr/covid19
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy
https://github.com/slzarate/parliament2
Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data.
Proper citation: Parliament2 (RRID:SCR_019187) Copy
Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource.
Proper citation: NEMAR (RRID:SCR_019100) Copy
http://synaptosoft.com/MiniAnalysis/ABFUtility.html
Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program.
Proper citation: ABF Utility (RRID:SCR_019222) Copy
Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.
Proper citation: OpenClinica (RRID:SCR_019223) Copy
http://www.neuro.uni-jena.de/cat/
Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.
Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy
https://CRAN.R-project.org/package=tidyverse
Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
Proper citation: tidyverse (RRID:SCR_019186) Copy
https://CRAN.R-project.org/package=NBR
Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.
Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy
Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.
Proper citation: long-read-tools (RRID:SCR_019116) Copy
Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.
Proper citation: BioSimulators (RRID:SCR_019111) Copy
https://jtremblay.github.io/amplicontagger.html
Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications.
Proper citation: AmpliconTagger (RRID:SCR_019112) Copy
https://bioconductor.org/packages/variancePartition/
Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.
Proper citation: variancePartition (RRID:SCR_019204) Copy
Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported.
Proper citation: Protein.Plus (RRID:SCR_019044) Copy
https://nrdg.github.io/fracridge
Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.
Proper citation: fracridge (RRID:SCR_019045) Copy
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