Tag Archives: embl

New and Updated Online Tutorials for ASTD, Entrez Protein and MMDB

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:

ASTD

  • 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

Entrez Protein

  • 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”

MMDB

  • 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
  • to locate and view structurally aligned homologs

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics.

About OpenHelix
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.

A shout out or two, Bork paper and on the shoulders of giants…

Just thought I’d give a shout out… two in fact:

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.

Second, Bora at Blog Around the Clock got together with gg of skullsinthestars and created a “The Giant’s Shouldersblog carnival. This grew out of the Classics Challenge  ( “read and research an old, classic scientific paper and write a blog post about it”) at skullinthestarts (which our own Mary had an excellent submission to if I do say so myself). It was so popular they decided to make it a monthly thing. Which is good, because now I can do the one I wanted to do before for August’s carnival. July’s carnival is here at Blog around the Clock.

New Tutorial Suite on SMART (protein domain analysis)

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.

About OpenHelix
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.

Speaking of the Bork lab…

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

Metagenomics

Just a short post with some information:

Metagenomics is the new genomics :). NIH Roadmap has a new initiative, the Human Microbiome Project with a bit of funding :) . Meanwhile, other projects and databases are developing such as Integrated Microbial Genomes w/ Microbiome Samples (or IMG/M) and Camera. It’s an exciting and fascinating field (my former colleagues at the Bork lab just published interesting research in this field), though some scientists of course have their doubts.