Tag Archives: resource

Tip of the Week: World Tour of Genomics Resources

Most weeks our tip is a five-minute movie that quickly introduces you to a new resource, or a cool new function at an established resource. Occasionally we feature one of our full resource tutorial that is being made freely available through resource sponsorship of our training suite. In this week’s tip we provide access to one of our tutorials that is especially near and dear to our heart. It is a World Tour of Genomics Resources in which we explore a variety of publicly-available biomedical, bioinformatics and bioscience databases and other resources.

This tutorial is quite different from our usual ones. Generally we focus on a specific software resource and describe step-by-step how to use its functions such as how to do basic and advanced searches, how to understand and modify displays, where to find specific types of data such as FASTA sequences, etc. and even provide tips on ‘hidden features’ that power users even find useful and informative.  This type of software training is absolutely critical.

But many people need an even earlier step: just the *awareness* that resources are available that might serve their needs. This tutorial fills that niche. We present a sampling of resources, all free to use, from each of 9 categories including: Analysis & Algorithms, Expression, Genome Browsers (for Eukaryotes and for Prokaryotes and Viruses), Genome VariationLiterature, Nucleotides, Pathways and Proteins. After the World Tour, which is the majority of the tutorial, we then describe how to use OpenHelix’s free search and learn portal to find bioscience resources most appropriate for your research needs. From this the tour transitions into a brief discussion of the format of our training materials and how to use them, and then ends with information about other learning resources that we provide.

This tutorial has been wildly popular whenever we’ve done it as a live seminar. At the NIH they actually had to lock the doors because we’d hit the capacity of the room, and people were turned away. In fact, it has been so popular that we decided to produce it as a full tutorial suite and release it as one of our free trainings so that anyone and everyone could learn about the breadth of great public software options available for free use.

In addition to this free tutorial, we also have published a paper entitled “OpenHelix: bioinformatics education outside of a different box” in a special issue of Briefings in Bioinformatics entitled “Special Issue: Education in Bioinformatics“. This paper describes a plethora of sources where researchers can access informal educational sources of learning on publicly available bioinformatics resources. The sources of information include a wide variety of formats including lists of resources, journals that regularly feature tool descriptions, and eLearning resources sources such as the MIT OpenCourseWare effort. If you know of other such resources that aren’t covered in our tour or paper, comment & let us know about them – we love to learn as much as we love to teach! :)

Quick link to World Tour of Genomics Resources tutorial here.

  • Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010). OpenHelix: bioinformatics education outside of a different box Briefings in Bioinformatics, 11 (6), 598-609 DOI: 10.1093/bib/bbq026

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.

Coat color genes

One of my favorite mailing lists is the mouse researcher discussion list at The Jackson Lab. I think is the list to which I have been subscribed the longest in my career. It is moderated (never spammed), it has a great community of mouse researchers, and they discuss a range of things–benchwork to bioinformatics. There are meeting announcements. Job postings. All sorts of stuff.

Today I learned that the Coat Color Genes web site has moved:

This useful WEB resource was created and maintained by Bill Oetting (Univ.
Minnesota) and offered through the IFPCS WEB page. Now, we have agreed with Bill that we will take over the responsability and, from now on, regularly update this WEB page. Please update your links accordingly.

Yesterday I learned that researchers are actually using Nair on mice to remove hair for bioimaging applications. Dark fur quenches signals, it turns out. This makes sense to me. But I had no idea that anyone still actually used Nair anymore. I didn’t even know they made it. See, you learn new things every day!

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

Eagerly awaiting the NAR database issue

For years I have been following the NAR database issue, watching the growth in the number of resources from a handful years ago to the hundreds lately. It is great to see what new resources have been added each year–there are people who are solving genomics problems in really creative ways.

Last year (2007) there were 968 resources listed, which was over a hundred more than the previous year (Galperin, Nucleic Acids Research, 2007, Vol. 35, Database issue D3-D4).I’m going to bet on over another hundred new ones this year, for a total of 1086.

Now I’m going over to look for new number in the advanced access section…. The Molecular Biology Database Collection: 2008 update and Michael Galperin reports on: 1078 databases. 110 more this year!

110…well, I will have to check them out and see who the new kids on the block are. I love new databases!