Tag Archives: wormbase

Video Tip of the Week: 3D Virtual Worm (encore)

Earlier this year I did a tip on the 3D Virtual Worm browser from the OpenWorm team. At that time, there wasn’t a publication to accompany that post. And since these tools get much more visibility when the posts go to ScienceSeeker and Research Blogging I wanted to revisit this now that there is a publication for this project.

One of the things I keep harping on is how much we need better visualization for the tremendous volumes of data we are going to have. Imagine the day when we can code the series of transcription-factor binding events followed by transcription evidence as cells differentiate into neurons. I can imagine it being just amazing to watch, but also providing insights into basic processes. That was true when the Virtual Cell team recently was coding up the cellular processes. Things they saw in the model helped refine the understanding of the biology, and vice versa. Understanding the initial steps better can also help us to look for ways to enhance tissue repair potentially. We’re a long way from this now, but some teams are working their way towards these strategies. It’s interesting to see what the data requirements are, and how crucial public data sets are for these projects. And projects like modENCODE will offer some of the necessary data foundations for that for worm, and I can see ENCODE and later projects doing that for virtual tissue culture cells someday.

In this paper the describe the work that has brought them to the point we find ourselves with the virtual worm. The schematic diagrams and the subsequent worm images are really compelling to look at and consider. And to note the crucial underlying benchwork studies that enable this to happen is important. Sometimes there’s tension between the bench and the computational perspectives on projects like “virtual” cells or organisms. But there’s undoubtedly room for both.

Here’s an earlier prototype of the features of this work from this team. It gives you a better sense of the innards of the process:

Certainly we are in an early phase of the work. But it’s important to head there, and it’s nice to see people thinking through the issues and working it out. And the worm 3D browser will continue to improve as groups like this team bring their work to the project.

Quick links:

Load the virtual worm and take a spin: http://browser.openworm.org/

More about the OpenWorm project:  https://code.google.com/p/openworm/

 Reference:

Palyanov, A., Khayrulin, S., Larson, S.D., & Dibert, A. (2012). Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment In Silico Biology, 11 (3), 137-147 DOI: 10.3233/ISB-2012-0445

Video Tip of the Week: A 3D Worm!

In this era of big data and computational tools, it’s easy to generate huge amounts of texty and statistical data that offers great insights into biology, and delivers leads to design experiments in actual organisms and cells. But the cell and developmental biologist in me still yearns for great visualization tools to explore the results, beyond rows and columns and p-values. I think that better visualizations of the “-omics” data is still one of the unmet needs in this arena, and I’ve talked about that more than once but most recently here.

I’ve been keeping an eye on the progress at WormBase because I knew that they were going to be changing over to their new interface soon (it’s there now and you should see the slick new look, and that means I have to update our tutorial once it’s all stable). So I was watching their blog for updates. One of the posts they had was for a different project, though, and I was really intrigued. They were touting the OpenWorm browser, which offers a 3D representation of a worm that you can interact with. I was hooked. Heh. (Hookworm–get it? Eh, nevermind….)

So I looked into the tool a bit more. There’s no publication on the current iteration (but it is referenced in the WormBase paper below), but I was reading up on some components and I watched the several videos on the OpenWorm site that talk in more detail about the goals and the project. The very enthusiastic talk by Stephen Larson comparing the worm to Lt. Data from StarTrek was quite engaging and accessible, and a nice demonstration of public outreach for complex science.

So, it’s not Lt. WormData yet exactly. But it’s a nice effort and I can see how it could be useful for visualizing complex data as it gets layered on to the physical structures. Transcription factor binding signals. Levels of expression of RNA-seq data. Opening chromatin. Protein modifications. All kinds of important biological stuff which I usually think of as “tracks” on genome browser could definitely be represented here. I hope it expands and that we can do these sorts of things for other organisms and cells and tissues.

And quite frankly it was just fun to drive it around. Check it out. Take this worm for a spin. And really–you can spin it… It looks like the future to me.

Quick links:

OpenWorm project information: http://www.openworm.org/

OpenWorm code project page: http://code.google.com/p/openworm/

OpenWorm 3D browser: http://browser.openworm.org

WormBase Virtual worm: http://caltech.wormbase.org/virtualworm/

WormBase (new site: http://www.wormbase.org ) and (legacy site: http://legacy.wormbase.org/)

Reference for WormBase:

Yook, K., Harris, T., Bieri, T., Cabunoc, A., Chan, J., Chen, W., Davis, P., de la Cruz, N., Duong, A., Fang, R., Ganesan, U., Grove, C., Howe, K., Kadam, S., Kishore, R., Lee, R., Li, Y., Muller, H., Nakamura, C., Nash, B., Ozersky, P., Paulini, M., Raciti, D., Rangarajan, A., Schindelman, G., Shi, X., Schwarz, E., Ann Tuli, M., Van Auken, K., Wang, D., Wang, X., Williams, G., Hodgkin, J., Berriman, M., Durbin, R., Kersey, P., Spieth, J., Stein, L., & Sternberg, P. (2011). WormBase 2012: more genomes, more data, new website Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr954

NAR database issue (always a treasure trove)

The advance access release of most of the  NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We’ll be writing up additional more extensive blog posts on it and doing some tips of the week over the next couple months, but I thought I’d highlight the issue and some of the reports:

There are a lot of updates to many of the databases we know and love (links to go full text article): UCSC Genome Browser, Ensembl, UniProt, MINT, SMART, WormBase, Gene Ontology,  ENCODE, KEGG, UCSC Archaeal Browser, IMG/M, DBTSS, InterPro and others (we have tutorials on all those listed here).

And, as an indication of the explosion of data available (itself a subject of a database issue article, SRA), there are a lot of new(ish) databases on specific datatypes such as MINAS, a database of metal ions in nucleic acids (nice name :D); doRiNA, a database of RNA interactions in post-transcriptional regulation; BitterDB, a database of bitter compounds and well over 100 more.

And I’ll give a special shout out to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu
Ensembl: http://www.ensembl.org/
UniProt: http://www.uniprot.org/
MINT: http://mint.bio.uniroma2.it/mint/
SMART: http://smart.embl.de/
WormBase: http://www.wormbase.org/
Gene Ontology: http://www.geneontology.org/
ENCODE: http://genome.ucsc.edu/ENCODE/
KEGG: http://www.kegg.jp
UCSC Archaeal Brower: http://archaea.ucsc.edu/
IMG: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
DBTSS: http://dbtss.hgc.jp/
InterPro: http://www.ebi.ac.uk/interpro

 

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Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • And we’ll monitor this so we can update our tutorial on WormBase when the new interface is out of beta and stable. RT @wormbase: Public beta period of the new WormBase website now open! http://bit.ly/qsLqCw and http://beta.wormbase.org/ #softlaunch #celegans [Mary]
  • RT @GenePattern: Announcing GParc: the GenePattern Archive. Share your modules and grow the GP community. http://bit.ly/fwlYqY #bioinformatics #genomics [Mary]
  • A predicted 9.3 billion people alive by 2050 – that’s hard for me to wrap my brain around. Special issue of Science (29 July 2011) deals with Population and Development, a lot of the content is open. [Jennifer]
  • RT @bffo: New COSMIC update includes update of Cancer Census Gene http://bit.ly/qXcI5L  #bioinformatics #cancer #genomics [Mary]
  • Medicinal plant genomes–very cool. PhytoMetaSyn: RT @mikesgene: Canadian scientists open gene database to public to help create new opportunities for biotechnology industry  http://bit.ly/nqPH6Q  #genome [Mary]
  • Man, I wanna play! Cool classroom resource for K-undergrad, per this Science article – “Beckman Institute’s Bugscope, http://bugscope.beckman.illinois.edu, a free educational technology outreach project, which enables kindergarten to 12th grade (K-12) and undergraduate students and teachers to remotely access and control the microscope in real time from their classroom computers.” [Jennifer]
  • Yay BioStar! RT @bioinformer: OpenSource bioinformatics tools are often so poorly documented, but @BioStarQuestion once again pulls through with what I needed. [Mary]
  • I just saw this press release” EDU-SCIENCE PREMIERS SCIENTIFIC AMERICAN
    BRANDED LINE OF SCIENCE TOYS AT FALL TOY PREVIEW IN DALLAS
    ” – but will they be available for Christmas? [Jennifer]
  • RT @eurogene: viewer looks interesting, now i need my genome MT @pathogenomenick: Tablet  – lots of plans for this excellent viewer http://bit.ly/mSEMkJ [Mary]
  • This is a nice little tool–custom genome diagrams: RT @NCBI: Upload your genome annotations, see them displayed on an ideogram and download an svg or eps file. http://1.usa.gov/mTGIze #genomics [Mary]

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
  • Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
  • Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
  • VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
  • A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
  • Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
  • On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Bioinformatics resource tweets

Yes, I know, but I used to be resistant to blogging too….

I’m starting to get a number of announcements about Twitter feeds from bioinformatics resource groups.  I think it’s time to start a collection of those.  This post will have a couple to get started, but I’m going to use this as a collector for others that will inevitably come across over time.

WormBase: (announcement), their feed is http://twitter.com/wormbase

GO: (announcement), their feed is http://twitter.com/news4go

If you have others, let me know in the comments. Or for my co-bloggers feel free to edit this post to grow the list.

Pointing us out at Genome.gov :)

ohonnhgripageNHGRI recently pointed out our new set of tutorials on model organism databases (funded mainly by NHGRI :) on their home page, genome.gov. Always nice to be recognized :D.

And it gives me the opportunity to again point out that we do indeed have seven publicly available tutorials and training materials (slides, exercises, etc) on model organism databases including SGD, RGD, MGI, WormBase, FlyBase and ZFIN… and a seventh on GBrowse, a generic genome browser used by some of these and other genome databases.

Check them out (and fill out the new poll to the left :D.

Tip of the Week: Model Organism Database tutorials

gbrowseFor the tip of the week today, we’d like to point out a number of new (free to you) tutorials on model organism database resources. These seven tutorials (include flash movie tutorial, slides for downloading, exercises and handouts) were partly funded by a NHGRI grant. We just put out a press release on this, but I thought the Tip of the Week would be a great place to introduce you to these tutorials. We have seven tutorials that are (or will soon be) publicly available (this link takes you to a list and links to all these tutorials). The first four available are on GBrowse, WormBase, RGD (Rat Genome Database) and MGI (Mouse Genome Informatics. GBrowse (the tutorial linked to here), was developed by the Generic Model Organism Database (GMOD) project and is a great tool to develop genome browsers for model and research organisms. Many model organism databases use GMOD resources in full or part, including many of the ones we have tutorials on here. Three more will be coming very soon on ZFIN (Zebrafish), FlyBase (Drosophila) and SGD (yeast). Check them out :).

Free Tutorials on Model Organism Genomic Databases Released by OpenHelix

OpenHelix today announced the free availability of tutorial suites on model organism databases and resources used extensively in research. The first tutorial suites available are GBrowse, Rat Genome Database (RGD), Mouse Genome Informatics (MGI), and WormBase. To be added in the coming weeks are Zebrafish Information Network (ZFIN), FlyBase and Saccharomyces (Yeast) Genome Database (SGD).

The tutorial suites, funded in part by a grant from the National Human Genome Research Institute of the National Institutes of Health, include a self run, narrated tutorial introducing the resource and how to use its feature and functions. Each suite also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others.

One of the first tutorials available is on GBrowse, developed by the Generic Model Organism Database (GMOD) project, a popular tool used by researchers to develop genome browsers for model organisms, species of interest, and particular topics. By learning how to use this “generic” genome browser, you can leverage that knowledge to use dozens of resources devoted to a wide range of research areas.

“The OpenHelix GBrowse user tutorial is very well done and will be an excellent resource for the many research communities that use GBrowse to visualize genomic data,” said Dave Clements of the National Evolutionary Synthesis Center who runs the GMOD help desk.

Model organisms, such as yeast, mouse, rat, flies, and many others, have long been used by researchers to expand our understanding of biology and to assess the effectiveness and safety of therapies before going to human trial. Many of the genomes of these organisms have been completely sequenced, giving the scientific community even greater insight into the organisms and their relation to human biology. The genome data is now available and searchable on publicly available online databases and resources.

You can view the Model Organism tutorials at http://www.openhelix.com/model_organisms.shtml. OpenHelix provides over 60 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix 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.

How to pick a genome database platform

I was reading a newsletter I get from Biotechniques, and their WebWatch often has some fun items. (You may need to get a free login to see the WebWatch.) This week they referred to the MaizeGDB database in the post Amaizing Base. Although I had been aware of MaizeGDB before, it was a nice reminder to go over and have a look to see what’s new.

When I went over there I was intrigued by the new browser they are about to launch (in mid-October). The link says “coming soon” and I went to check out the information there.

Currently that link goes to a page that describes their move to a more sequence-centric representation of their data. It was a fascinating look at their decision process to move to a new browser platform and what they decided to do. For database geeks like me, seeing their ranking of the importance of various features was very compelling.

And what they decided? GBrowse!

We have a tutorial available on GBrowse. Usually we do tutorials on specific sites, but as we kept seeing GBrowse over and over at different sites we created a tutorial for that. It helps me to understand the underlying basic browser when I visit any site that employs it. Even though the wrappings and the data types will vary at different sites, understanding how it works makes it much easier to use at any new site that uses it. HapMap, MGI, WormBase, FlyBase, TAIR, Watson’s personal genome, and a whole bunch of other sites use the GBrowse software.

Looking forward to checking out the MaizeGDB GBrowse version when it launches!