Curator Dashboard

Magazine published by Simbios, a National NIH Center for Biomedical Computing, covering the latest research wherever computation, biology, and medicine intersect. In addition to disseminating information about the latest research in biomedical computation, they aim to foster community amongst the wide audience interested in any and all aspects of biomedical computing. Whether you are a long time researcher in this area or new to it, please consider joining those who have already started to participate in Biomedical Computation Review. You are encouraged to: * Write a letter to the editor on any relevant topics * Suggest your favorite topics that should receive more attention * Suggest an idea for a feature article * Propose an idea for an Under the Hood tutorial * Tell us any other way in which we can better serve this community

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• SciCrunch
• 16 years ago - by Anonymous

A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.

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• SciCrunch
• 13 years ago - by Anonymous

We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation.

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• SciCrunch
• 16 years ago - by Anonymous

Public research university in Leeds, West Yorkshire, England. It was established in 1874 as the Yorkshire College of Science. In 1884 it merged with the Leeds School of Medicine and was renamed Yorkshire College.

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• SciCrunch
• 17 years ago - submitted by Christie Wang

Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program.

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• SciCrunch
• 13 years ago - by Anonymous

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.

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• SciCrunch
• 16 years ago - by Anonymous

Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

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• SciCrunch
• 16 years ago - by Anonymous

The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or genomic data should credit the Stanley Medical Research Institute, as well as any individual SMRI collaborators whose data is being used. Publications which make use of analytic results/methods in the database should additionally cite Dr. Michael Elashoff. Registration is required to access the data.

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• SciCrunch
• 15 years ago - by Anonymous

Data set of over 1500 one- and two-minute EEG recordings, obtained from 109 volunteers. Subjects performed different motor/imagery tasks while 64-channel EEG were recorded using the BCI2000 system (http://www.bci2000.org). Each subject performed 14 experimental runs: two one-minute baseline runs (one with eyes open, one with eyes closed), and three two-minute runs of each of the four following tasks: # A target appears on either the left or the right side of the screen. The subject opens and closes the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the left or the right side of the screen. The subject imagines opening and closing the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject opens and closes either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject imagines opening and closing either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. The data are provided here in EDF+ format (containing 64 EEG signals, each sampled at 160 samples per second, and an annotation channel).

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• SciCrunch
• 16 years ago - by Anonymous

Reference atlas of Brodmann Areas in the Human Brain with an Emphasis on Vision and Language. Other Pages include: Flat Brodmann Maps, Brodmann Area Names (with locational Descriptions), Flat Visual Area Maps, Language Areas, PopUp Gyri Maps

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• SciCrunch
• 15 years ago - by Anonymous

Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples)

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• SciCrunch
• 15 years ago - by Anonymous

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

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• SciCrunch
• 16 years ago - by Anonymous

Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases.

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• SciCrunch
• 15 years ago - by Anonymous

siDirect 2.0 provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5'' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for > 94% of human mRNA sequences in RefSeq. Enter an accession number and retrieve sequence or Paste in a nucleotide sequence.

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• SciCrunch
• 16 years ago - by Anonymous

One of four health sciences units within Mercer Health Sciences Center. Provides the first pharmacy program in the region to offer the Doctor of Pharmacy degree as its sole professional degree. The College offers the Doctor of Pharmacy (Pharm.D.) degree and the Doctor of Philosophy (Ph.D.) degree in pharmaceutical sciences, as well as four combined degree programs – Pharm.D./M.B.A, Pharm.D./M.P.H., Pharm.D./Ph.D. and Pharm.D./M.S. in Health Informatics.

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Java-based software that blasts each sequence that you provide it, and then looks for a consensus taxon among the top-hits returned from blast. MARTA uses NCBI''s megablast program to align your sequence(s) against a local installation of blast. Then MARTA uses GenInfo Identifiers from the top-hits to retrieve taxonomic information from NCBI''s taxonomy database. Using your thresholds/cutoffs, MARTA ''votes'' to find a taxonomic assignment by consensus; MARTA might resolve some sequences to species level, and others to kingdom or to no level, depending on the taxonomic information held within your tag or sequence.

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• SciCrunch
• 13 years ago - by Anonymous

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

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• SciCrunch
• 15 years ago - by Anonymous

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

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• SciCrunch
• 13 years ago - by Anonymous

The Rocky Mountain Tissue Bank is a Colorado, 501c3 non-profit corporation, established in 1980. It is governed by a Board of Directors and is an independent tissue processing facility with no affiliation with any other tissue bank. It develops and produces irradiated allogenic cancellous bone and marrow for human transplantation. This product stimulates bone regeneration in patients with bone loss due to trauma, disease, or genetic malformation and provides a foundation for dental implants. The primary distribution network is through Periodontists, and Oral Surgeons and clinicians specializing in implant dentistry.

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• SciCrunch
• 16 years ago - by Anonymous