Curator Dashboard

A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

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• SciCrunch
• 13 years ago - by Anonymous

An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.

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• SciCrunch
• 13 years ago - by Anonymous

A database that provides quantitative real time (qRT) PCR primers for 99.96% human RefSeq sequences. For 99% of intron-bearing genes, the PCR product will cross an exon-exon border which overlaps one of the largest introns. Primers are assumed to have a uniform annealing temperature of 60C, allowing them to be used in large-scale assays.

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• SciCrunch
• 17 years ago - by Anonymous

Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available. <BR/> Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.

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• SciCrunch
• 16 years ago - by Anonymous

The academic programs and scientific research interests in our department cover a wide range of topics, with special emphasis on Cell Biology, Neurobiology, Developmental Biology, Physiology, Anatomy, Biophysics, and Neuroinformatics. Together, faculty and students in our department study biological processes that span the continuum from single cells to the entire human body. The Department of Cell Biology and Neuroscience offer both an Undergraduate and Graduate Program, which includes Ph.D. or M.S. degrees in Neuroscience or Biological Science. Two different undergraduate degree options are available within the Cell Biology and Neuroscience major: Biomedical Sciences and Cell Biology & Neuroscience. The Department of Cell Biology and Neuroscience offers exciting opportunities to work with nationally and internationally recognized faculty on a wide range of research topics, including cognitive neuroscience, neurophysiology, neuroinformatics, developmental biology, cell biology, biophysics and computational neuroscience.

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• SciCrunch
• 17 years ago - by Anonymous

The Department of Neurosciences is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities. The teaching mission of our Department effectively communicates the current state of knowledge in neuroscience to the medical, graduate, and post-graduate students of the University using innovative methods. We are nationally known for using the most current technologies to teach human anatomy, embryology, and neurobiology to medical and graduate students. We teach critical thinking and problem solving skills and also provide opportunities for the students to excel in the laboratory and develop as life-long learners. Faculty participate in our Neurosciences and Neurological Disorders (NND) training track which awards both Ph.D. and M.S. degrees. We also train students towards the M.D./Ph.D and M.D./ M.S.B.S. joint degrees. Our research mission incorporates molecular, cellular, and systems neuroscience and cuts across the boundaries of traditional departments and disciplines. Our funded research in neurodevelopment, neurodegeneration, regeneration and repair, sensory function, and drug abuse comprise just a few of our interests. We employ cutting edge technologies and focus on the solution of fundamentally important problems pertinent to nervous system diseases and processes that can be translated feasibly to clinical issues. We work towards a synergistic interaction between the clinical and basic sciences that prompts unexpected discoveries of causes and novel treatments for the diseased nervous system. We also coordinate the Human Body Donation Program at the University of Toledo College of Medicine.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )

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• SciCrunch
• 17 years ago - by Anonymous

Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

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• SciCrunch
• 13 years ago - by Anonymous

A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development.

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• SciCrunch
• 17 years ago - by Anonymous

An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO).

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• SciCrunch
• 13 years ago - by Anonymous

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.

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• SciCrunch
• 13 years ago - by Anonymous

A structured controlled vocabulary for the representation of plant environmental conditions.

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• SciCrunch
• 13 years ago - by Anonymous

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

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• SciCrunch
• 17 years ago - by Anonymous

Department that trains independent, creative, productive scholars in the physiological sciences. The department offers programs leading to the Ph.D. degree. A combined M.D./Ph.D. or D.M.D./Ph.D. degree program is available for students who obtain prior or concurrent admission to the Schools of Medicine or Dentistry respectively. The primary research interests of the department are Cardiovascular Physiology, Endocrinology, and Neuroscience. Physiology faculty currently hold more than $7,000,000 in extramural funding, ranking 21st out of Medical School Physiology Departments nationally. Members of the Department teach in the Medical and Graduate Schools including Medical Physiology and Intergated Systems Biology, Neuroscience and advanced courses in cardiovascular and endocrine physiology.

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• SciCrunch
• 17 years ago - by Anonymous

Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

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• SciCrunch
• 17 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented January 28, 2019. Core Facility provides the software and support for computer assisted protein and DNA sequence analysis and database access. The Genetics Computer Group GCG-Wisconsin package is currently available on PBRC's UNIX platform that is accessible via modem or direct connection. The package can be accessed via three interfaces: the command-line interface (UNIX C-shell), the web-based interface (SeqWeb) and the X-Windows based graphics interface (SeqLab). Applications in the package include sequence editing, alignment, comparison, primer design, restriction analysis, mapping, data presentation, database browsing, etc. In addition to local databases, access to remote databases (BLAST) is integrated into the package. The local databases are updated quarterly. Databases available include GenBank, EMBL, PIR-Protein, SWISS-PROT and Restriction Enzymes (REBASE).

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• SciCrunch
• 15 years ago - by Anonymous

Research and development project at Stanford University to create a standards-based informatics platform supporting clinical and translational research. STRIDE consists of three integrated components: a clinical data warehouse, based on the HL7 Reference Information Model (RIM), containing clinical information on over 1.6 million pediatric and adult patients cared for at Stanford University Medical Center since 1995; an application development framework for building research data management applications on the STRIDE platform and a biospecimen data management system. STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships. STRIDE receives clinical data for research use via HL7 feeds from both SUMC hospitals: Lucile Packard Children's Hospital and Stanford Hospital and Clinics. This clinical data is used to support a wide variety of translational research services including: * Anonymized Patient Research Cohort Discovery * Electronic Chart Review for Research * IRB-Approved Clinical Data Extraction * Biospecimen Data Management * Multimedia Research * Data Management and Research Registries STRIDE is a highly secure environment utilizing encryption, fine-grained access control, robust auditing and detailed data segregation. Additionally, STRIDE has a robust access control framework with well-defined access granting authorities and access control groups. Consequently STRIDE meets or exceeds the requirements of the HIPAA Privacy and Security regulations. Privacy protection is further enhanced by requiring IRB approval for all research projects using STRIDE clinical data. From a technology and standards perspective, STRIDE is hosted on the Oracle 11g database platform. STRIDE application software provides access to the web services of a three-tier infrastructures using SSL encryption with strong authentication. These programs are cross-platform, self-updating thick-client applications that provides a rich user interface for data entry, retrieval and review as well as image manipulation and annotation. STRIDE makes extensive use of XML technologies for representation of structured meta data, distributed systems technologies using JSON for secure remote communication between client and server, and Swing graphical interface components providing a rich widget-set as well as advanced imaging and graphing capabilities. Users of the STRIDE Research Desktop Client can perform rapid data entry into structured fields, compose complex queries, and interact securely with clinical, research and imaging data.

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• SciCrunch
• 17 years ago - by Anonymous