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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://genome.unmc.edu/ngLOC/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

Proper citation: ngLOC (RRID:SCR_003150) Copy   

•   Source: SciCrunch Registry

http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry

http://www.morphbank.net/

An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.

Proper citation: MorphBank (RRID:SCR_003147) Copy   

•   Source: SciCrunch Registry

http://bioit.fleming.gr/mrb/

Dynamic and interactive view of 222 world wide available mouse resources, classified in 22 categories. The massive generation of data has led to the propagation of mouse resources and databases and the concomitant need for formalized experimental descriptions, data standardization and database interoperability and integration. In this context and with these goals, information is collected through an online questionnaire and/or manual curation. All mouse resource data in MRB are broken up in four sections and presented in four tabs: * The General section/tab contains information such as URL(s), contact information, database description and categorization and related links. * The Ontologies & Standards tab indicates controlled vocabularies and data representation standards adopted by each resource, such as ontologies and minimum information standards. A hyperlink to an index of OBO and non-OBO ontologies can be found here; an index of minimum information standards can be found here. * The Technical tab holds technical information for each resource such as the server technology used, relational database management system(s) utilized, programming language(s) of implementation, schema descriptive documents or actual database dumps and most importantly information on each resource''s programmatic access, the integration and interoperability services. Additionally and through the integration with Molgenis, MRB is capable of generating a SOAP API for hosted resources. * The final section on Database Description Framework (DDF) Criteria, describes the compliance of each resource to the CASIMIR database criteria, which aim to capture key technical data about a database in a formal framework. All data in MRB are freely available to interested users through downloadable weekly database dumps. Programmatic access to some of MRB''s data is feasible via MRB''s SOAP web service. MRB is the front end of a relational, fully normalized PostgreSQL database. The source code is available under the GNU general public license (GPL) as a binary download and via cvs.

Proper citation: MRB - Mouse Resource Browser (RRID:SCR_005961) Copy   

•   Source: SciCrunch Registry

https://neuroscienceblueprint.nih.gov/Resources-Tools/Blueprint-Resources-Tools-Library

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.

Proper citation: Biomedical Informatics Research Network (RRID:SCR_005163) Copy   

•   Source: SciCrunch Registry

http://www.elra.info/

ELRA is the driving force to make available the language resources for language engineering and to evaluate language engineering technologies. In order to achieve this goal, ELRA is active in identification, distribution, collection, validation, standardization, improvement, in promoting the production of language resources, in supporting the infrastructure to perform evaluation campaigns and in developing a scientific field of language resources and evaluation. ELRA''s missions are to promote language resources for the Human Language Technology (HLT) sector, and to evaluate language engineering technologies. To achieve these two major missions, we offer a range of services, listed below and described in the Services around Language Resources section: - Identification of language resources - Promotion of the production of language resources - Production of language resources - Validation of language resources - Evaluation of systems, products, tools, etc., related to language resources - Distribution of language resources - Standardization The promotion of the production of language resources also includes our support of the infrastructure for evaluation campaigns and our support in developing a scientific field of language resources and evaluation, e.g. via the LREC conference. ELRA also regularly conducts market studies and surveys in the field of HLT, and publishes a quarterly newsletter, distributed not only to its members but also to a large number of people in the HLT community.

Proper citation: European Language Resources Association (RRID:SCR_004909) Copy   

•   Source: SciCrunch Registry

http://vmd.vbi.vt.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.

Proper citation: VMD (RRID:SCR_004905) Copy   

•   Source: SciCrunch Registry

http://www.pristionchus.org

This data resource is a genetic, molecular, and genomic toolkit that establishes one particular species, Pristionchus pacificus, as a major satellite system for evolutionary developmental biology. Users may download Pristionchus Sequences and use the Pristionchus pacificus genome browser where they may find gene or gene prediction data. Users can also use the BLAST feature, which allows users to search the assembly for position information of bacs, reads and contigs using the mapping tool. The center of the site's research is the evolutionary analysis of vulva formation. The general aim of the Department is to develop the nematode vulva as a suitable case study into the evolutionary alterations of developmental processes. By studying and comparing two distantly related species of the same phylum, such as P. pacificus and C. elegans, macroevolutionary alterations of developmental processes and mechanisms can be identified. The final goal of the Department is to achieve a comprehensive description of macro- and microevolutionary changes of developmental mechanisms at the molecular level in a phylogenetic and ecological context.

Proper citation: Pristionchus.org (RRID:SCR_003414) Copy   

•   Source: SciCrunch Registry

http://htseq.readthedocs.io/en/release_0.9.1/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

Proper citation: HTSeq (RRID:SCR_005514) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/behavior-ontology

An ontology consisting of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending the GO process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. The prime application of NBO is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes. The main ontology is available in both the OBO Flatfile Format and the Web Ontology Language (OWL).

Proper citation: Neurobehavior Ontology (RRID:SCR_006201) Copy   

•   Source: SciCrunch Registry

http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

•   Source: SciCrunch Registry

http://seer.cancer.gov/resources/

Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.

Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy   

•   Source: SciCrunch Registry

http://www.gbif.org/

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of countries and organizations, GBIF promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet. GBIF provides three core services and products: # An information infrastructure an Internet-based index of a globally distributed network of interoperable databases that contain primary biodiversity data information on museum specimens, field observations of plants and animals in nature, and results from experiments so that data holders across the world can access and share them # Community-developed tools, standards and protocols the tools data providers need to format and share their data # Capacity-building the training, access to international experts and mentoring programs that national and regional institutions need to become part of a decentralized network of biodiversity information facilities. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity. GBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers. * Explore Species: Find data for a species or other group of organisms. Information on species and other groups of plants, animals, fungi and micro-organisms, including species occurrence records, as well as classifications and scientific and common names. * Explore Countries: Find data on the species recorded in a particular country, territory or island. Information on the species recorded in each country, including records shared by publishers from throughout the GBIF network. * Explore Datasets: Find data from a data publisher, dataset or data network. Information on the data publishers, datasets and data networks that share data through GBIF, including summary information on 10028 datasets from 419 data publishers.

Proper citation: GBIF - Global Biodiversity Information Facility (RRID:SCR_005904) 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://f1000.com/posters

An open access repository of conference posters from across the life sciences and medicine. It provides a permanent, structured environment for the deposition of posters as well as a trustworthy venue for ongoing discussion and development of the information being presented. You can browse posters by Topic or Section or by conference. Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed. The most interesting posters are selected for evaluation by our expert Faculty and you will receive ideas and feedback. Widen your audience ����?? top performing posters receive 800+ views in a month!

Proper citation: F1000 Posters (RRID:SCR_006503) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.8/bioc/html/qrqc.html

Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

Proper citation: qrqc (RRID:SCR_006867) Copy   

•   Source: SciCrunch Registry

Issue

https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

http://www.chem.qmul.ac.uk/iubmb/enzyme/

Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes by the reactions they catalyze. Also included are links to individual documents and advice is provided on how to suggest new enzymes for listing, or correction of existing entries. The common names of all listed enzymes are listed, along with their EC numbers. Where an enzyme has been deleted or transferred to another EC number, this information is also indicated. Each list is linked to either separate entries for each entry or to files with up to 50 enzymes in each file. A start has been made in showing the pathways in which enzymes participate. For other enzymes a glossary entry has been added which may be just a systematic name or a link to a graphic representation. The glossary from Enzyme Nomenclature, 1992 may also be consulted. This has been updated with subsequent glossary entries. Each enzyme entry has links to other databases. Enzyme Subclasses provide links to a list of sub-subclasses which in turn list the enzymes linked to separate files for each enzyme, or to a list as part of a file with up to 50 enzymes per file.

Proper citation: Enzyme Nomenclature (RRID:SCR_006583) Copy   

•   Source: SciCrunch Registry

https://www.aplysia.earth.miami.edu/

Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration.

Proper citation: National Resource for Aplysia (RRID:SCR_008361) Copy   

•   Source: SciCrunch Registry