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http://www.GeneWeaver.org

Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Proper citation: Gene Weaver (RRID:SCR_003009) Copy   

•   Source: SciCrunch Registry

http://burgundy.cmmt.ubc.ca/cgi-bin/RAVEN/a?rm=home

Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RAVEN (RRID:SCR_001937) Copy   

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http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/

IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file.

Proper citation: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature (RRID:SCR_006027) Copy   

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http://www.kaluefflab.com/znpindex.html

Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted.

Proper citation: Zebrafish Neurophenome Project Database (RRID:SCR_004482) Copy   

•   Source: SciCrunch Registry

http://zebrafish.org

Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.

Proper citation: Zebrafish International Resource Center (RRID:SCR_005065) Copy   

•   Source: SciCrunch Registry

http://www.textpresso.org/

An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.

Proper citation: Textpresso (RRID:SCR_008737) Copy   

•   Source: SciCrunch Registry

http://crezoo.crt-dresden.de/crezoo/

Database of helpful set of CreERT2 driver lines expressing in various regions of the developing and adult zebrafish. The lines have been generated via the insertion of a mCherry-T2A-CreERT2 in a gene trap approach or by using promoter fragments driving CreERT2. You can search the list of all transgenic lines or single entries by insertions (gene) or expression patterns (anatomy/region). In most cases the CreERT2 expression profile using in situ hybridization at 24 hpf and 48 hpf is shown, but also additional information (e.g. mCherry or CreERT2 expression at adult stages, transactivation of a Cre-dependent reporter line) is displayed. Currently, not all insertions have been mapped to a genomic location but the database will be regularly updated adding newly generated insertions and mapping information. Your help in improving and broadening the database by giving your opinion or knowledge of expression patterns is highly appreciated.

Proper citation: CreZoo (RRID:SCR_008919) Copy   

•   Source: SciCrunch Registry

http://crispr.dbcls.jp/

Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.

Proper citation: CRISPRdirect (RRID:SCR_018186) Copy   

•   Source: SciCrunch Registry

http://neuromorpho.org/index.jsp

Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

Proper citation: NeuroMorpho.Org (RRID:SCR_002145) Copy   

•   Source: SciCrunch Registry

http://zebra.sc.edu/index.html

A portal to different zebrafish resources such as jobs, book, journals, database, meetings, and K-12 programs. Most information leads to ZFIN: The Zebrafish Model Organism Database.

Proper citation: Zebrafish Information Server (RRID:SCR_002237) 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://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) Copy   

•   Source: SciCrunch Registry

https://monarchinitiative.org/

Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN.

Proper citation: MONARCH Initiative (RRID:SCR_000824) Copy   

•   Source: SciCrunch Registry

http://genenet2.uthsc.edu/geneinfoviz/search.php

GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool

Proper citation: GeneInfoViz (RRID:SCR_005680) Copy   

•   Source: SciCrunch Registry

http://zfin.org/zf_info/anatomy/dict/sum.html

A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.

Proper citation: Zebrafish Anatomical Ontology (RRID:SCR_005887) Copy   

•   Source: SciCrunch Registry

http://www.webgestalt.org/

Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

Proper citation: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) Copy   

•   Source: SciCrunch Registry

http://edwardslab.bmcb.georgetown.edu/

The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.

Proper citation: Edwards Lab (RRID:SCR_008860) Copy   

•   Source: SciCrunch Registry

http://akt.ucsf.edu/EGAN/

Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible

Proper citation: EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) Copy   

•   Source: SciCrunch Registry

http://zebrafish.wi.mit.edu/rnai/

Community built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board.

Proper citation: Zebrafish RNAi Database (RRID:SCR_008965) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/about/sources/nlx_143622-1

International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly.

Proper citation: One Mind Biospecimen Bank Listing (RRID:SCR_004193) Copy   

•   Source: SciCrunch Registry