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http://databrary.org/

Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.

Proper citation: Databrary (RRID:SCR_010471) Copy   

•   Source: SciCrunch Registry

http://mvz.berkeley.edu/

The Museum of Vertebrate Zoology (MVZ) at the University of California, Berkeley, is a center for research and education in the biology of amphibians, reptiles, birds, and mammals. Founded in 1908, the Museum''s mission is to document and increase understanding of the diversity of terrestrial vertebrates, with particular emphasis on western North America. An MVZ Video Gallery is also available. The superb collections are at the heart of the MVZ program, where methods of field biology are combined with modern laboratory techniques and analytical methods in a comprehensive, synthetic approach. Our goals are to remain at the forefront of international research on evolutionary biology from the perspectives of systematics, ecology, behavior, functional and developmental morphology, population biology, and evolutionary genomics, and to lead the way in developing and using major natural history collections for research, education, and solving problems in biodiversity conservation. Because the MVZ was founded upon a philosophy that organisms should be studied in relationship to their natural environments, its collections are supplemented by extensive ancillary information (e.g., field notes, habitat photographs, tape-recorded vocalizations) that is connected to specimens and/or tissues and enhances their value to researchers. This concept was pioneered at the MVZ and continues to be the primary focus of current research efforts. To this end, there are strong research links between the Museum and the 2,000 acre MVZ/UC field station at Hastings Natural History Reservation. In addition, the MVZ is actively engaged in developing concepts and tools for Biodiversity Informatics through collaborations across the Berkeley Natural History Museums and international consortia.

Proper citation: Museum of Vertebrate Zoology (RRID:SCR_010595) Copy   

•   Source: SciCrunch Registry

http://www.clinfowiki.org/wiki/index.php/Main_Page

A Wiki devoted to topics in clinical informatics. Contents: 1 Health Information Technology Regional Extension Centers 2 Free and Open Source Software (FOSS) licensing in medicine 3 Electronic Healthcare Communication 4 Electronic Medical Record (EMR) Systems 5 Computer-based Provider Order Entry -- CPOE 6 Clinical Decision Support -- CDS 7 Books on Topics in Clinical Informatics 8 Medical Devices, Computerized -- SmartDevices 9 Personal Health Records -- PHRs 10 Personal Health Applications -- PHAs 11 Informatics Students'' Contributions 12 Blueprint for a Comprehensive HIT System 13 Biobanking -- a.k.a. Biorepositories or Tissue Banks 14 Organizational issues 15 Regional Health Information Organizations -- RHIOs 16 Evidence-Based Medicine -- EBM 17 Evaluation Methods in Informatics 18 Unintended Consequences of Health Information Technology 19 Quality & Quality Informatics 20 Public Health Informatics 21 U.S. Federal Health Information Technology Initiatives 22 The E-Patient-Provider Relationship 23 Interface Terminology 24 New CIS-related Technologies 25 Workflow 26 Terminology and Coding 27 Interface/Usability Testing 28 International views 29 Blogposium, April 2006 30 Departments / Schools of Biomedical or Medical Informatics 31 Endowed Professorships and Chairs in Health / Medical / Nursing / Biomedical Informatics 32 Leading Health Informatics and Medical Informatics Journals o 32.1 Ranking of ISI/SCI listed e-Health and Medical Informatics Journals o 32.2 Not listed / ranked in ISI/SCI 33 External Links 34 External Medical Reference Links 35 External Informatics Organizations Links

Proper citation: Clinical Informatics Wiki (RRID:SCR_010518) Copy   

•   Source: SciCrunch Registry

http://www.geneious.com/

Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.

Proper citation: Geneious (RRID:SCR_010519) Copy   

•   Source: SciCrunch Registry

http://jjwanglab.org/snvrap

The web portal provides comprehensive local database of human genome variants with a user-friendly web page that provides a one-stop annotating and funtonal prediction service which is both convenient and up-to-date. A query can be accepted as either a dbSNP Id or a chromosomal location and our system will instantly provide all the annotation information in an interactive LD panel. The system can also simultaneously prioritize this variant based on additive effect mode by corresponding annotation information and evaluate the variant effect that is then displayed in a prioritization tree. Furthermore, cohort sequencing continuously produces lots of un-annotated variants such as rare variants or de novo variants, and our system can even fit this data by accepting genomic coordinates (hg19) to offer maximal annotations. Main Functions Over 40 up-to-date annotation items for human single nucleotide variations; Functional prediction for different types of variants; Dynamic LD panel for both HapMap and 1000 Genomes Project populations; Prioritization score and tree viewer based on variant functional model.

Proper citation: SNVrap (RRID:SCR_010512) Copy   

•   Source: SciCrunch Registry

https://medschool.ucsd.edu/Pages/default.aspx

Graduate medical school of University of California, San Diego. It was the third medical school in the University of California system, after those established at UCSF and UCLA, and is the only medical school in the San Diego metropolitan area.

Proper citation: University of California San Diego School of Medicine; California; USA (RRID:SCR_010634) Copy   

•   Source: SciCrunch Registry

http://www.abbvie.com/

A research-based biopharmaceutical company that develops advanced therapies to address global health problems.

Proper citation: AbbVie (RRID:SCR_010484) Copy   

•   Source: SciCrunch Registry

http://www.cff.org/

The mission of the Cystic Fibrosis Foundation, a nonprofit donor-supported organization, is to assure the development of the means to cure and control cystic fibrosis and to improve the quality of life for those with the disease. The Foundation is the leading organization in the United States devoted to cystic fibrosis. It funds and accredits more than 115 CF care centers, 95 adult care programs and 50 affiliate programs, and more than 75 chapters and branch offices nationwide. The Cystic Fibrosis Foundation is one of the most efficient organizations of its kind and is an accredited charity of the Better Business Bureau''s Wise Giving Alliance. Until we conquer this disease, our team will work tirelessly to extend and enhance life for those with cystic fibrosis by functioning as: * Scientific pioneers, blazing new trails in CF research; * Fund-raisers, securing the money needed to support our efforts; * Advocates, keeping CF a top priority in government, industry and research; * Investors, funding drug discovery and development; * Caregivers, linking patients and families to specialized CF care; and * Family, offering support, information and resources.

Proper citation: Cystic Fibrosis Foundation (RRID:SCR_010726) Copy   

•   Source: SciCrunch Registry

http://www.grenoble.prabi.fr/obiwarehouse

OBIWarehouse (Open Biological Warehouse) aims at integrating several biological data sources into a unified database. Content includes 3D structural data, Protein-related data, Metabolic-related data, Genomic-related data, and Biological classification.

Proper citation: OBIWarehouse (RRID:SCR_010729) Copy   

•   Source: SciCrunch Registry

http://bcb.cs.tufts.edu/dflat/

We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining.

Proper citation: DFLAT (RRID:SCR_010738) Copy   

•   Source: SciCrunch Registry

http://www.cbil.upenn.edu/cgi-bin/tess/tess

TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page.

Proper citation: TESS: Transcription Element Search System (RRID:SCR_010739) Copy   

•   Source: SciCrunch Registry

http://mirtar.mbc.nctu.edu.tw/human/

An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.

Proper citation: miRTar (RRID:SCR_010851) Copy   

•   Source: SciCrunch Registry

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+srsq2+-noSession

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search.

Proper citation: SRS (RRID:SCR_010736) Copy   

•   Source: SciCrunch Registry

http://wanglab.pcbi.upenn.edu/coral/

A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.

Proper citation: CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) Copy   

•   Source: SciCrunch Registry

http://paed.hku.hk/uploadarea/yangwl/html/software.html

A toolkit for prioritizing SNVs and indels from next-generation sequencing data.

Proper citation: PriVar (RRID:SCR_010784) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/CNVer/

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.

Proper citation: CNVer (RRID:SCR_010820) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/cnvnator/

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Proper citation: CNVnator (RRID:SCR_010821) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/diplotyper/

A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression.

Proper citation: Diplotyper (RRID:SCR_010789) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/freec/tutorial.html

Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.

Proper citation: Control-FREEC (RRID:SCR_010822) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/readdepth/

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

Proper citation: readDepth (RRID:SCR_010824) Copy   

•   Source: SciCrunch Registry