Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources.
Seattle, WA September 24, 2008 — OpenHelix today announced the availability of new tutorial suites on the Alternative Splicing and Transcript Diversity (ASTD) database, Entrez Protein and the Molecular Modeling Database (MMDB). ASTD is an European Bioinformatics Institute (EBI) resource for alternative splice events and transcripts for the human, mouse, and rat systems. Entrez protein is a comprehensive database of protein information brought to you by the National Center for Biotechnology Information (NCBI). MMDB is another NCBI resource which contains an extensive collection of three-dimensional protein structures with detailed annotation that can be used to learn about the structure and function of many proteins. Together these three tutorials give the researcher an excellent set of resources to carry their research from transcript to 3d protein structure.
The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:
to perform Quick and Advanced searches
to navigate gene and transcript report pages
to predict intron/exon boundaries and likely regulatory protein binding site
to search manually curated data regarding alternate splicing
to perform basic and advanced searches utilizing the many available tools and options
to understand the protein records and exploit the many internal and external links you are provided with
to explore some of the resources provided by the NCBI network of databases, such as “My NCBI”
to search MMDB using both basic and advanced query techniques
to understand the detailed results you obtain
to visualize and manipulate structures using NCBI’s Cn3D structural viewer
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.
First, my former Postdoc advisor, Peer Bork, and lab just published an excellent paper in Science entitled “Drug Target Indentification Using Side-Effect Similarity.” It’s an excellent example of the marriage of computational genomics and experimental biology. Fascinating stuff (I’m only slightly biased, but it is). I’ll do a more in depth review later.
Comprehensive Tutorial on the SMART Bioinformatics Resource enables researchers to quickly and effectively use invaluable resource.
January 11, 2008 (Seattle WA) OpenHelix today announced the availability of a tutorial suite on the SMART bioinformatics resource (http://smart.embl-heidelberg.de/). SMART, created by the Bork Lab at the European Molecular Biology Laboratory (EMBL), contains information on hundreds of domains, and provides extensive annotations, phylogenetic analyses, and links to relevant resources about the domains.The tutorial suite, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contains a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorial, researchers can quickly learn to effectively use this resource that helps them understand the evolution of function within multi-domain proteins. SMART brings together several functions that a researcher would otherwise have to perform separately.The tutorial will teach users to:
perform various text and sequence searches
find proteins based on their domain architecture
browse for key information about the evolutionary history and relationships of domains of interest to your researchTo find out more about this and other tutorial suites visit www.openhelix.com.
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.
In the previous post I briefly mentioned a paper coming out of the Bork lab at EMBL.
The lab just made public a new tool: STITCH, “a resource to explore known and predicted interactions of chemicals and proteins.” This is a sister project to STRING, a great tool for exploring the interactions of proteins