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http://www.acgtinc.com

Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

Proper citation: ACGT Inc. (RRID:SCR_001026) Copy   

•   Source: SciCrunch Registry
  

http://datacite.labs.orcid-eu.org

Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite.

Proper citation: ODIN (RRID:SCR_001386) Copy   

•   Source: SciCrunch Registry
  

http://neuralensemble.org/sumatra/

A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt.

Proper citation: Sumatra (RRID:SCR_001381) Copy   

•   Source: SciCrunch Registry
  

http://craigmod.com/

Blog by Craig Mod: Thinking about the future of books and publishing and story telling.

Proper citation: Craig Mod (RRID:SCR_000609) Copy   

•   Source: SciCrunch Registry
  

http://www.butterflybase.org

An open-access Genomic Database for Lepidoptera. It includes all the Lepidoptera cDNA sequences available in NCBI's dbEST. Support for genomic-DNA sequences such as BACs and the Bombyx mori genome is being generated. Tools available on this website include BLAST search, Annotation search, Primer design, and Microsatellite repeat finders. Users can also download all data and sequences. Within the site, the Expressed Sequence Tag sequences are made with Trace2dbest from raw sequence data if available or downloaded from NCBI. We cluster them using PartiGene into gene-objects to reduce redundancy. Subsequently, we perform hierarchical BLAST searches to provide accurate similarity annotation and a robust protein translation protocol using prot4EST. Putative proteins objects have been further annotated with the Gene Ontology biological vocabulary (GO terms) and InterPro (EBI) domains to facilitate gene-hunters. The repository is open for all Lepidopteran researchers.

Proper citation: ButterflyBase (RRID:SCR_000727) Copy   

•   Source: SciCrunch Registry
  

http://www.cangem.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September23, 2022. Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. Within the website, users can browse microarray data or perform searches by hospital/disease classification/pathology/clinical presentation and other methods.

Proper citation: Cancer GEnome Mine (RRID:SCR_000728) Copy   

•   Source: SciCrunch Registry
  

http://massgenomics.org/

Blog discussing next-generation sequencing and medical genomics in the post-genome era. Most posts are in-depth reviews of recent research publications or editorials.

Proper citation: MassGenomics (RRID:SCR_001018) Copy   

•   Source: SciCrunch Registry
  

http://cellularscale.blogspot.com/

Blog focusing on cellular-level neuroscience for everyone. While a higher level of neuroscience, such as behavioral studies and human fMRI scans level of neuroscience is interesting to everyone, some people might want to focus a little closer in. That is what The Cellular Scale is for.

Proper citation: Cellular Scale (RRID:SCR_001379) Copy   

•   Source: SciCrunch Registry
  

http://biozon.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. It currently provides data on pairwise similarities between proteins, the domain structure of proteins, structural similarities, threading-based and profile-profile similarities between protein families. Additional information about 3D models, predicted protein-protein interactions, assignment of genes to pathways and expression data analysis, as well as local and global maps of the protein space will be gradually added to Biozon.

Proper citation: Biozon (RRID:SCR_000725) Copy   

•   Source: SciCrunch Registry
  

http://www.nih.gov/science/models/rat/

The Rat Genome Program was launched after the National Institutes of Health (NIH) realized the potential of rat models in understanding basic biology and human health and disease. The purpose of this NIH Rat Genomics and Genetics web site is to serve as a central point for information on NIH sponsored and related rat genetic and genomic activities and resources. It will provide information on: the follow up to recommendations made to the NIH; funding opportunities for rat genomic and genetic tools and resources; major rat genomic resources available and/or produced in response to the NIH Rat Program; courses and meetings related to rat genomics and genetics; and selected reports and publications. These programs have produced a wide variety of resources and a way to link and capitalize upon the data and resources of other model organisms and the human. In conjunction with and in addition to these programs, the NIH, through the RGWG, has convened advisory groups and workshops to discuss the opportunities that rat models offer and provide recommendations on the investments that are needed to capitalize on these opportunities.

Proper citation: NIH Rat Genomics and Genetics (RRID:SCR_002267) Copy   

•   Source: SciCrunch Registry
  

http://sarst.life.nthu.edu.tw/cpdb/

A database of circular permutation (CP) in proteins that provides resources for studying circular permutation (CP) and circular permutation relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments.

Proper citation: CPDB - the Circular Permutation Database (RRID:SCR_002261) Copy   

•   Source: SciCrunch Registry
  

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry
  

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry
  

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17493288

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. LinkHub is a software system using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. It leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data. For efficiency, it is also provided with relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; LinkHub was used to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as connecting glue between different identifier spaces. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code. Sponsors: Funding for this work comes from NIH/NIGMS grant P50 GM62413-01, NIH grant K25 HG02378, and NSF grant DBI-0135442.

Proper citation: LinkHub: A Semantic Web System that facilitates cross-database queries and information retrieval in proteomics (RRID:SCR_001844) Copy   

•   Source: SciCrunch Registry
  

http://mech.ctb.pku.edu.cn/protisa/

Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

Proper citation: ProTISA (RRID:SCR_002138) Copy   

•   Source: SciCrunch Registry
  

http://django.nubic.northwestern.edu/fundo/

Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.

Proper citation: FunDO (RRID:SCR_001725) Copy   

•   Source: SciCrunch Registry
  

https://epd.expasy.org/epd/

Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

Proper citation: Eukaryotic Promoter Database (RRID:SCR_002132) Copy   

•   Source: SciCrunch Registry
  

http://caps.ncbs.res.in/stifdb2/

Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.

Proper citation: STIFDB (RRID:SCR_002131) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/swissprot/hpi/hpi.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals.

Proper citation: Human Proteomics Initiative (RRID:SCR_002373) Copy   

•   Source: SciCrunch Registry
  

http://www.cisreg.ca/tfe

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

Proper citation: Transcription Factor encyclopedia (RRID:SCR_002130) Copy   

•   Source: SciCrunch Registry