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Research institute that focuses on basic biomedical science, drug discovery and technology development. The Scripps Florida research team focuses on the development of therapeutics in areas including neurology, cancer, the immune system, cardiovascular disease, metabolic disease, and infectious diseases. This institute has six departments: Cancer Biology, Molecular Therapeutics, Immunology and Microbial Science, Metabolism and Aging, Chemistry, and Molecular and Integrative Neurosciences. There is also the Translational Research Institute (TRI) which includes the following components: Discovery Biology, Drug Metabolism and Pharmacokinetics (DMPK), TRI-Informatics, Lead Identification and HTS, and Medicinal Chemistry. These groups collaborate in the discovery and development of new therapeutic agents. The Scripps Florida institute also offers a graduate program that emphasizes chemistry, chemical biology, biophysics and the biological sciences. This resource also provides a variety of programs for middle school, high school and college-age students to participate in research activities. These programs have a special emphasis on recruiting from historically underrepresented groups in the sciences.

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• SciCrunch
• 17 years ago - by Anonymous

Vivisimo''s mission is to help organizations maximize the business value of their information through innovations in search and discovery technology. Building on its other innovations, Vivisimo was first to offer enterprise social search, which lets enterprise users share their knowledge with coworkers by tagging, ranking, and annotating search results. Vivisimo''s founders first developed new ways to categorize search results as a research project at Carnegie Mellon University''s computer science department. After years of product development and further innovations, Vivisimo today offers Velocitya complete enterprise search platform that unifies access to secure business repositories, presents search results with an unmatched user experience, and enables knowledge sharing across an organization. Velocity is making single-search-box access to wide selections of corporate information a reality at organizations large and small. You can install Velocity in minutes, use its web console to configure access to diverse document, email, database, and web page repositories, and import their access rights so that searchers get just what they''re authorized to see and nothing more. Use the console to spotlight high-value information, package repositories into search tabs, enable clustered results by topic or meta-data, enliven the search results with embedded images, and more, all without custom programmingjust configuration.

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• SciCrunch
• 17 years ago - by Anonymous

The Molecular Biology and Genetics Department at Bogazii University is one of the major reference laboratories in Turkey, specialized in molecular analysis of common genetic disorders. Over the years, the rapid accumulation of mutation data in connection with detailed clinical and laboratory information, has led to the idea of establishing a national database for storing, analysing and presenting it in a more efficient and systematic way. For this purpose, an interdisciplinary project was initiated in 1995. b-Thalassemia and Hemophilia-B Databases were selected as preliminary models, for they offer alternative design and implementation strategies due to different clinical and genetic characteristics. b-Thalassemia is an autosomal recessive disorder, characterized by microcytosis and hemolytic anemia, which is the result of reduced b-Globin chain synthesis. In Turkey, the disease is represented with a gene frequency of 2 and reflected by a wide spectrum of clinical manifestations with the presence of more than 40 different mutation. Currently, there is no database available for thalassemia mutations. Hemophilia B is an X-linked recessive disorder caused by heterogenous mutations, resulting in a marked deficit of coagulation factor IX (FIX); an essential component of the clotting mechanism. A hemophilia B database was first published in 1990 as a list of point mutations and short additions and deletions with 115 mutations comprising 216 entries Gene-, System-, or Disease- Specific Databases

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Toxics Release Inventory (TRI), a resource of the U.S. Environmental Protection Agency, is a set of publicly available databases containing information on releases of specific toxic chemicals and their management as waste, as reported annually by U.S. industrial and federal facilities. This inventory was established under the Emergency Planning and Community Right to Know Act of 1986 (EPCRA). TRI''s data, beginning with the 1987 reporting year, covers air, water, land, and underground injection releases, as well as transfers to waste sites. In agreement with the Pollution Prevention Act of 1990, source reduction and recycling data is also included in TRI. The Toxicology and Environmental Health Information Program (TEHIP) in the Division of Specialized Information Services (SIS) of the National Library of Medicine (NLM) provides access to TRI as part of its TOXNET (TOXicology Data NETwork) databases, which cover toxicology, hazardous chemicals, environmental health and related areas.

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• SciCrunch
• 17 years ago - by Anonymous

Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.

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• SciCrunch
• 17 years ago - by Anonymous

It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction.

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• SciCrunch
• 17 years ago - by Anonymous

Silkbase''s objective is to build a foundation for the complete genome analysis of Bombyx mori.

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• SciCrunch
• 17 years ago - by Anonymous

Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.

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• SciCrunch
• 16 years ago - by Anonymous

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

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• SciCrunch
• 17 years ago - by Anonymous

Literature database on disability and rehabilitation maintained by the National Rehabilitation Information Center. The database describes over 80,000 documents covering physical, mental, and psychiatric disabilities, independent living, vocational rehabilitation, special education, assistive technology, law, employment, and other issues as they relate to people with disabilities. The collection spans 1956 to the present. Full text search is supported.

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• SciCrunch
• 17 years ago - by Anonymous

Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26,2019. Portal that provides information about and links to immunostaining agents, protocols, discussion forums and an image gallery. Immunohistochemical Staining Immunohistochemistry (IHC) is a technique for identifying cellular or tissue constituents (antigens) by means of antigen-antibody interactions, the site of antibody binding being identified either by direct labelling of the antibody, or by use of a secondary labelling method. In Situ Hybridization (ISH) techniques allow the demonstration of specific nucleic acid sequences (genes) in their cellular environment.

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• SciCrunch
• 17 years ago - by Anonymous

PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything; gene names, diseases, gene functions, authors, etc. The user can then quickly sort or browse the frequency matrix table to do individual searches independently. This allows the user to build up tables of word relationships in PubMed in the context of your experiments or your scientific interests. This is useful for analyzing combinatorial datasets, as found with multiplex experimental systems, such as cDNA microarrays, genomic, proteomic, or other multiplex comparisons. The PubMatrix database is an archive of previous searches on many topics. Sponsors: PubMatrix is supported by the National Institutes of Health.

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• SciCrunch
• 17 years ago - by Anonymous

PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 30, 2015. Refer to Proteome Analyst 3.0. Subcellular Localization and GO General Molecular Function predictions for many model organism proteomes using Protein Analyst, with a very high coverage rate. When users blast their proteins against the database of results, they will not only be shown blast homologs from the model organisms, but also the Subcellular Localization and GO General Molecular Function predictions as well.

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• SciCrunch
• 17 years ago - by Anonymous

The Protein Coil Library is a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database. The Protein Coil Library allows rapid and comprehensive access to non-alpha-helix and non-beta-strand fragments contained in the Protein Data Bank (PDB). The library contains both sequence and structure information together with calculated torsion angles for both the backbone and side chains. Several search options are implemented, including a query function that uses output from popular PDB-culling servers directly. Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state. The library stores the complete torsion angle descriptions for the fragments as well as the three dimensional structures of the fragments themselves. The goal of extracting and pre-calculating this data is to allow for more straightforward investigation of peptide structure without the background of secondary structure elements. In addition to searching by PDB ID, it is possible to download a particular size class, perform a batch search of PDB/chain ID''s, or download precompiled lists of PDB ID''s of interest (PDB Select, etc.). For users interested in browsing the entire database at once or maintaining their own locally-updated copy of the library, FTP access instructions are also provided. The files stored in the coil library FTP site or returned after a batch search are organized heirarchically by PDB ID. This is done to reduce filesystem access times and fascilitate searches using the UNIX find utility. At the lowest directory level in the heirarchy, files are further sorted by fragment length. As a result, the number of files in a particular directory is generally less then 50, yielding relatively fast access on UNIX/Linux filesystems. The heirarchical organization is based on the middle two letters of the PDB ID. For example, hen egg lysozyme, which has a PDB ID of 1HEL, will be located in the directory h/he/. At the final level, fragments of varying sizes are stored in directories that correspond to their fragment length. Again, using lysozyme as an example, any seven-residue fragments, if they exist, will reside in the directory h/he/7/. Similarly, seven-residue fragments from 2HEX and 1HE0 will also be in this location. Sponsors: The Protein Coil Library is funded by Johns Hopkins University.

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• SciCrunch
• 17 years ago - by Anonymous

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

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• SciCrunch
• 17 years ago - by Anonymous

Species 2000 is a federation of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world''s species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms. Each database covers all known species in the group, using a consistent taxonomic system. The participating databases are widely distributed throughout the world and currently number 52. The existing global species databases presently account for some 60% of the total known species, so substantial investment in new databases will be needed for full coverage of all taxa to be achieved.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products.

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• SciCrunch
• 17 years ago - by Anonymous

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

• Resource
• SciCrunch
• 17 years ago - by Anonymous