Tag Archives: SGKB

SBKB – New Name, Same Great Resource + More!

The PSI-Nature Structural Genomics Knowledgebase (SGKB) that we’ve posted on before has been rebranded to now be named the PSI-Nature Structural Biology Knowledgebase (SBKB), provided to you by the Protein Structure Initiative (PSI). The new branding just rolled out yesterday, along with the September issue of all the features, and a reorganized left navigation area that organizes pages by scientific focus.

But don’t fear, the FREE SGKB tutorial by OpenHelix that you know and love still accurately demonstrates how to use the search functions of the SBKB, and we are currently working to update our tutorial to reflect the new branding and the new navigation options. Stay tuned for an announcement about the release of the updated SBKB tutorial soon!

Tip of the Week: PSI Structural Genomics Knowledgebase

Last January I did a tip that featured the monthly Structural Genomics Update, which is essentially a newsletter and article collection from PSI Structural Genomics Knowledgebase (SGKB). However, the update is just one aspect of what SGKB offers. In today’s tip I want to feature the wonderfully efficient ways that Structural Genomics Knowledgebase provides you with to learn about the proteins that you are interested in. What I tried to stress in this tip is the different emphasis that Structural Genomics has compared to the RCSB PDB. The RCSB PDB is a GREAT resource, which we also have free tutorial on, but it was created by and for structural biologists. Its displays feature angstroms, angles, conformers and more.

Me, I’m a Molecular Biologist by training & I think about proteins in terms of genomes, pathways, medical relevance, molecular functions, and the like. The SGKB thinks like me, and even organizes information and links into those sorts of categories. I really like how it presents protein information to me, and in the process how it eases me into thinking about the more ‘hard core’ structural details that I see in PDB. The tip is just a teaser taste of the SGKB – if I peak your interest, please do check out OpenHelix’s full, free introductory tutorial on the PSI-SGKB (sponsored by PSI SGKB) as well as the site itself. You never know, you might just learn to love a crystal! :^)

Education at NCBI

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally :), a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.

PSI SGKB v2.0 has been released!

I noticed today that the Protein Structure Initiative has released an updated version of their Structural Genomics Knowledgebase. I have been looking forward to the release of these features since I got to explore them at their beta site while making our introductory tutorial on the resource. As I’ve blogged about before, I like this site & think many of their tools and offerings are unique and quite useful for a wide variety of bioscience users.

You can read their announcement about what is new here, and follow links to our free tutorial on using the PSI SGKB. Alternatively you can visit the landing page for our tutorial, link to the resource, download our training materials or launch our tutorial movie. Regardless of the route you take, I suggest you check out the updates to this great resource!

Quick Reference Cards for teaching and outreach

We know there are a number of different ways that scientists and students become familiar with genomics software.   Some of it comes from the traditional publication routes–like the very handy NAR Database issue.  Or like the Current Protocols papers we’ve done recently.  We have these online tutorials that people use in various ways: some teach themselves by watching the video and working the exercises, some download the matching slide sets and run local workshops (our catalog: some are free/sponsored and green icons indicate that; red indicates subscription required). Librarians are using them to become “embedded” in courses in some cases.

A less-well-known type of material we have is the Quick Reference Card.  These are printed cards with URLs, hints, tips, definitions, shortcuts–for stuff that you may want a quick reminder of: where a feature is located, or how to use it.  People who run the local workshops will sometimes write to us to get a set for their courses.  They are great to give out at conferences to raise awareness of the software.

We have these cards for several resources that we also have free sponsored training videos + slides + exercises with: UCSC Genome Browser (2 cards–intro and table browser); Galaxy, and our newest: RCSB PDB and SGKB.  You can go to this form and order them, and we’ll send them out.

I bring this up today because we just received word from Ensembl that they have created a card that we can distribute as a PDF.  You can print it up and put it on the wall near the computer as a handy reminder of some features and tools at Ensembl.  Click the image to download the PDF, or go directly to the link below.

Summary:

Order OpenHelix printed cards for resources: http://www.openhelix.com/cgi/qrcOrder.cgi

Ensembl PDF card download: Ensembl_card_march2010.pdf

Quick note: SGKB and PDB tutorials

We recently announced a free tutorial (sponsored by PSI) on the Structural Genomics Knowledgebase (SGKB). I thought it might be of interest to our readers. You can access the free tutorial (approx. a 1hr movie, slides, handouts and exercises) here.

We will also soon announce a free tutorial on the Protein Database (PDB), but you can already access it here.

For a full list of our free tutorials and training materials, click here (about a dozen), or view our other 80 or more tutorials on a wide range of topics by subscription.

The Protein Structure Initiative announces free OpenHelix tutorial and training materials for the Structural Genomics Knowledgebase (SGKB)

Free tutorial and training materials available for the Structural Genomics Knowledgebase bionformatics resource

Working with OpenHelix to provide online training materials and increased visibility is an effective way to add to our efforts

Bellevue, WA (PRWEB) March 18, 2010 — The Structural Genomics Knowledgebase(SGKB), a one-stop shop for information about proteins hosted at Rutgers University, has partnered with OpenHelixTM to provide free comprehensive training and outreach programs for its online protein “portal” located at http://kb.psi-structuralgenomics.org.

The SGKB is a free, comprehensive resource produced through a collaboration between the National Institutes of Health’s Protein Structure Initiative and Nature Publishing Group. The PSI SGKB contains genetic, structural, functional and experimental information about proteins that is easily accessible through a variety of reports and displays. The portal also includes links to many additional resources.

“Structural genomics is fast emerging as an essential tool in expanding our knowledge of the role of proteins in biology and in disease,” said OpenHelix founder and CSO Dr. Warren Lathe. “OpenHelix is excited to contribute to furthering this field by assisting researchers in effectively and efficiently using this powerful resource.”

The new training initiatives include a free online tutorial suite on how to use/search/find/etc. the SGKB.

The online narrated tutorial runs in just about any browser and can be navigated in a number of ways. In about 60 minutes, the tutorial highlights and explains the features and functionality needed to start using the SGKB effectively. The tutorial can be used by new users to introduce them to the protein portal, by previous users to view new features and functionality or simply as a reference tool to understand specific features.

In addition to the tutorial, SGKB users can also access useful training materials, including the animated PowerPoint slides used as a basis for the tutorial, suggested talking points for the slides, slide handouts and exercises. This can save a tremendous amount time and effort for educators looking to create classroom content.

Users can view the tutorials and download the free materials at http://www.openhelix.com/sgkb .

OpenHelix also has created a free Quick Reference Card for the SGKB. The Quick Reference card highlights search strategies, features and functionality. The cards can be ordered in packs of 30 from www.openhelix.com, and shipping is free within the United States.

“The SGKB sets itself apart by incorporating so many different types of biological data (genetic, structural, theoretical, functional, protocol, etc.) that is really is a ‘one-stop shop’ for a broad range of biological and biomedical fields. The challenge for training and outreach is to make this data accessible and understandable to scientists across different disciplines,” said Dr. Helen Berman, head of the SGKB. “Working with OpenHelix to provide online training materials and increased visibility is an effective way to add to our efforts.”

In addition to the SGKB tutorial suite, OpenHelix offers nearly 90 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorial suites are freely available through support from the resource providers. The whole catalog of tutorial suites is available through a subscription. Users can view the tutorials and download the free materials atwww.openhelix.com.

About the PSI
The Protein Structure Initiative (PSI, http://www.nigms.nih.gov/Initiatives/PSI/), which is supported by the National Institutes of Health, is a federal, university and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of the PSI is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. The PSI strives to gain biological insights from new structures and to help the broad biomedical research community make use of PSI research findings.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Tip of the Week: PSI SGKB’s Monthly Structural Genomics Update (Edited)

In today’s tip I’d like to show you the monthly Structural Genomics Update from the Protein Structure Initiative  Structural Genomics Knowledgebase or PSI SGKB. Some of you may not be aware of the PSI SGKB, but it is a resource related to the RCSB PDB resource, which is very well known. We are currently creating a tutorial that will feature the whole knowledgebase & we will be sure to let you know when that is available. Today I want to feature their monthly Structural Genomics Update, which provides a great collection of articles and features related to structural genomics and protein biology as a whole. The Update is produced by Nature Publishing Group in collaboration with the Protein Structure Initiative.

I cannot begin to cover the full functionality of the SGKB in this tip, so go over there & explore it, watch for our tutorial to come out, maybe even add an SGKB widget (Trey talked about it here) to your web site!  Also, feel free to let me know what your favorite part of the PSI SGKB is, when you get a chance. Enjoy the tip!

EDIT: If you tried to watch this tip yesterday & had trouble, it was not on your end. Apparently there was some glitch part way through during my upload (thanks for the heads up, Greg!). I’ve reloaded the movie file & it plays through now, so please try it again – this is a great resource that should not be missed!

Widgets are cool

RCSB has put goether a PDB Comparison Tool Widget .


I put in 2K9G and 1ZLM, two SH3 domains. Used chain A for both and blast2seq as comparison algorithm (there are several choices), and these are my results. I’m not promising any biological significance to my choices and results, but the widget works nicely and simply. I can see it as a nice addition to someone’s homepage.

There are some other 3rd party widgets over at PDB such as this SGKB widget which you can get at the link above and the Mac dashboard widget you can download (and I always like Mac biology widget!).

Which got me to thinking, there must be other widgets out there for embedding into web sites. I found this Ontology one, anyone else know of any? Perhaps I can put together a widget page! for fun.