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General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education.
Proper citation: General Neural Simulation System (RRID:SCR_006316) Copy
Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies.
Proper citation: JStor Global Plants (RRID:SCR_025018) Copy
https://github.com/caaswxb/SRY
Software application for sorting long-read of sex-limited (Y or W) chromosome. Used to identify male specific k-mers based on population data.
Proper citation: Sorting long Reads of Y or other sex-limited chromosome (RRID:SCR_025036) Copy
Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded.
Proper citation: Adult Zebrafish Brain Gene Expression Database (RRID:SCR_025122) Copy
https://github.com/JustinChu/ntsm
Software alignment free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection. Used to count number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to compute the probability that sample are of the same origin to discover incongruent samples or sample swaps.
Proper citation: ntsm (RRID:SCR_024994) Copy
https://compbio.uth.edu/FusionGDB2/
Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level.
Proper citation: FusionGDB2 (RRID:SCR_025299) Copy
https://medinform.jmir.org/2015/4/e35
Algorithm for generating unique study identifiers in distributed and validatable fashion, in multicenter research. Light-weight, block chain style resource identifier generation for tracking resource linkage, provenance, utilization, and visualization. NHash has unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about study participant for research purposes; (2) it can be generated automatically in completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates set of cryptographic hash functions based on N-grams, with combination of additional encryption techniques such as shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers.
Proper citation: NHash Identifier (RRID:SCR_025313) Copy
Provides catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast and fission yeast. Data have been collated as culmination of number of genome-wide studies to identify location of replication origins throughout budding yeast genome. In addition to genome-wide studies data from large number of other origin mapping and characterization studies have been included.
Proper citation: OriDB (RRID:SCR_025365) Copy
https://github.com/tovaroe/GBMatch_CNN/
Software tool for predicting TS and risk from glioblastoma whole slide images. Used to predict risk scores and transcriptional subtypes from whole slide images of glioblastomas.
Proper citation: GBMatch_CNN - GBMPredictor (RRID:SCR_025316) Copy
https://snp.icgrc.info/cannseek
Database of Cannabis sativa Single Nucleotide Polymorphisms discovered from NGS sequences and BioSamples available in NCBI. Sequence reads were called against cs10, Purple kush, and Finola reference assemblies using GATK and Parabricks pipelines.
Proper citation: CannSeek Database of Cannabis sativa SNPs (RRID:SCR_025579) Copy
Portal built for the release and sharing of data resources of "Big Earth Data Science Engineering Program (CASEarth)" launched by the Chinese Academy of Sciences. A global raster data of land cover and land use. This data can be used for mapping and spatial modeling in Geographic Information Systems (GIS) or other computer programs. This website is not accessible from the USA.
Proper citation: Chinese CASEarth Data Sharing and Service Portal (RRID:SCR_025660) Copy
https://polymerscreen.yale.edu
Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein.
Proper citation: MAP Database Guide for Membrane Protein Solubilization (RRID:SCR_025656) Copy
A raster layer of global vegetation types, in Chinese. Please note the website is not functional from the US.
Proper citation: Chinese National Earth System Science Data Center (RRID:SCR_025658) Copy
Web app for global DEM data with spatial resolution of about 30m. This data can be used for mapping and spatial modelling in GIS or other computer programs.
Proper citation: Chinese Geospatial Data Cloud (RRID:SCR_025659) Copy
Public archive of raw sequence data in National Genomics Data Center as part of the China National Center for Bioinformation. GSA accepts worldwide data submissions, performs data curation and quality control for all submitted data. Provides data storage and sharing services.
Proper citation: Chinese Genome Sequence Archive (RRID:SCR_025826) Copy
Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage.
Proper citation: MorphoSource (RRID:SCR_025654) Copy
https://discover.nci.nih.gov/cellminer/
Database and query tool designed for cancer research community to facilitate integration and study of molecular and pharmacological data for the NCI-60 cancerous cell lines. The NCI-60, panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen over 100,000 chemical compounds and natural products since 1990.
Proper citation: CellMiner (RRID:SCR_025648) Copy
https://subtiwiki.uni-goettingen.de/
Comprehensive database about Gram-positive model bacterium Bacillus subtilis. Provides curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways.
Proper citation: SubtiWiki (RRID:SCR_025748) Copy
https://sipi.usc.edu/database/
Collection of digitized images.Maintained primarily to support research in image processing, image analysis, and machine vision.
Proper citation: USC-SIPI Image Database (RRID:SCR_025683) Copy
Openly licensed platform to work with RNA-RNA and protein-RNA interactions with software and pipelines to deeply mining thousands of high-throughput sequencing data of RNA-RNA interactome, CLIP-seq and degradome sequencing.
Proper citation: Encyclopedia of RNA Interactomes (RRID:SCR_025686) Copy
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