Tag Archives: genomics resources

Announcement of Updated Tutorial Materials: UniProt, Overview of Genome Browsers, and World Tour of Resources

As many of you know, OpenHelix specializes in helping people access and utilize the gold mine of public bioscience data in order to further research.  One of the ways that we do this is by creating materials to train people – researchers, clinicians, librarians, and anyone interested in science - on where to find data they are interested in, and how to access data at particular public databases and data repositories. We’ve got over 100 such tutorials on everything from PubMed to the Functional Glycomics Gateway (more on that later).

In addition creating these tutorials, we also spend a lot of time to keep them accurate and up-to-date. This can be a challenge, especially when lots of databases or resources all have major releases around the same time. Our team continually assesses and updates our materials and in this post I am happy to announce recently released updates to three of our tutorials: UniProt, World Tour, and Overview of Genome Browsers.

Our Introductory UniProt tutorial shows users how to: perform text searches at UniProt for relevant protein information, search with sequences as a starting point, understand the different types of UniProt records, and create multi-sequence alignments from protein records using Clustal.

Our Overview of Genome Browsers introduces users to introduce Ensembl, Map Viewer, UCSC Genome Browser, the Integrated Microbial Genomes (IMG) browser, and to the GBrowse software system. We also touch on WebGBrowse, JBrowse, the Integrative Genomics Viewer (IGV), the ARGO Genome Browser, the Integrated Genome Browser (IGB)GAGGLE, and the Circular Genome Viewer, or CGView.

Our World Tour of Genomics Resources is free and accessible without registration. It includes a tour of example resources, organized by categories such as Algorithms and Analysis tools, expression resources, genome browsers (both Eukaryotic and Prokaryotic/Microbial) , Literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation. This main discussion will then lead into a discussion of how to find resources with the free OpenHelix Resource Search Portal, followed by learning to use resources with OpenHelix tutorials, and a discussion of additional methods of learning about resources.

Quick Links:

OpenHelix Introductory UniProt tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=77

OpenHelix Overview to Genome Browsers tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=65

Free OpenHelix World Tour of Genomics Resources tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=119

 


Video Tip of the Week: Big Changes to NCBI’s Genome Resources


NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been developed, it has become obvious that new types of information (such as expanded metadata) need to be collected, and new ways of handling data are required.

NCBI has been adapting to such needs throughout the years and recently has been adapting its genome resources. Today’s tip will be based on some of those changes. My video will focus on the “completely redesigned Genome site”, which was recently rolled out and announced in the most recent NCBI newsletter. I haven’t found a publication describing the changes, but the newsletter goes into some detail and the announcement found at the top of the Genome site (& that I point out in the video) has very helpful details about the changes.

As you will see in the announcement, the Genome resource is not the only related resource to have undergone changes recently, including the redesign of the Genome Project resource into the BioProject resource and the creation of the BioSample resource. I won’t have time to go into detail about those two resources but at the end of my post I will link to two recent NCBI publications that came out in Nucleic Acids Research this month – these are good resources to read for more information on BioProject, BioSample, and on the NCBI as a whole. For a historical perspective I also link to the original Genome reference, which is in Bioinformatics and currently free to access.

Some of the changes are very interesting, including that “Single genome records now represent an organism and not a genome for one isolate.” The NCBI newsletter states that “Major improvements include a more natural organization at the level of the organism for prokaryotic, eukaryotic, and viral genomes. Reports include information about the availability of nuclear or prokaryotic primary genomes as well as organelles and plasmids. ” There’s also a note that “Because of the reorganization to a natural classification system, older genome identifiers are no longer valid. Typically these genome identifiers were not exposed in the previous system and were used mainly for programmatic access. ” That makes me wonder what changes this will mandate to other NCBI’s resources, as well as external resources. I haven’t seen any announcements on that yet, so I’ll just have to stay tuned & check around often.

Enjoy the tip & let us, or NCBI, know what you think of their changes! :)

Quick Links:

NCBI Homepage: http://www.ncbi.nlm.nih.gov/

Entrez Genome Resource Homepage: http://www.ncbi.nlm.nih.gov/genome

BioProject Resource Homepage: http://www.ncbi.nlm.nih.gov/bioproject/

References:

Historic Entrez Genome reference: Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999). Complete genomes in WWW Entrez: data representation and analysis Bioinformatics, 15 (7), 536-543 DOI: 10.1093/bioinformatics/15.7.536

Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T., Yaschenko, E., & Ostell, J. (2011). BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata Nucleic Acids Research DOI: 10.1093/nar/gkr1163

Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., Feolo, M., Fingerman, I., Geer, L., Helmberg, W., Kapustin, Y., Krasnov, S., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Karsch-Mizrachi, I., Ostell, J., Panchenko, A., Phan, L., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., Wilbur, W., Yaschenko, E., & Ye, J. (2011). Database resources of the National Center for Biotechnology Information Nucleic Acids Research DOI: 10.1093/nar/gkr1184

OH Newsletter

OpenHelix has had a newsletter for the last couple years. We send it to subscribers and others interested. It’s a bit of an open secret :). Well, I (Trey) took over putting it together this year and am in the midst of doing our latest one, I thought I’d mention it on the blog.

The newsletter comes out 3-4 times a year. We highlight a few of our more popular or interesting Tips of the Week, write a short article and update subscribers on the new tutorials we’ve added or recently updated ones. Regular readers of this blog will probably already have already gotten much of this if they keep up on the tips or the OH on the right hand column, but it might be a good way to remind yourself of some of our tips, or to get in one place all the tutorials we’ve updated or added in the past 3-4 months.

You can subscribe here and you can view the last or past newsletters here. A new one is coming out in a couple weeks!

Washington University Subscribes to OpenHelix Training Portal

Researchers, faculty, students and staff at Washington University can now efficiently and effectively learn to use bioinformatics and genomics resources with the extensive tutorial suite catalog from OpenHelix.

Bellevue, WA (PRWEB) April 26, 2010 — Bernard Becker Medical Library at Washington University School of Medicine has purchased a subscription to OpenHelix (www.openhelix.com) giving faculty, students and staff access to over 90 tutorial suites on bioinformatics and genomic resources.

With OpenHelix tutorials, Becker Library offers the Washington University community a quick and effective way to learn about the most powerful and popular genomics and bioinformatics databases and resources. These tutorials cover many types of resources including protein databases, bioinformatics analysis tools, model organism databases, SNP databases, comparative genomics, pathway and interaction resources and much more. “We’re thrilled that we are able to provide such a fantastic suite of resources to our research community,” said Kristi Holmes, PhD bioinformaticist at Becker Medical Library. “These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program.”

These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program

The online narrated tutorials, which run in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain the features and functionality needed to start using the resources effectively. The tutorial can be used by new users to introduce them to a resource, or by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, users also have access to useful training materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount of time and effort for teachers and professors creating classroom content.

“It is difficult, and certainly cost prohibitive, for university Libraries to create and provide training on the many critical genomic resources available,” said Scott Lathe, Chief Executive Officer of OpenHelix. “With an OpenHelix subscription, Washington University provides an efficient and effective training solution for their researchers.”

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.

Coming up, Guest Posts

Greetings! OpenHelix Blog is instituting a new semi-weekly feature. Every Wednesday we have our “Tip of the Week,” on Thursdays we have our “What’s Your Problem,” and now on an occasional Tuesdays we are going to have our “Provider Guest Post.” These will be posts from providers of genomics tools and database and will be opinions, updates and upcoming features of the resource, whatever the provider of the resource would like to convey to users. We have several lined up for the coming weeks, so keep checking back.

Additionally, if you are a developer or provider of an free, publicly available genomics or biological resource, database or analysis tool and would like to post in our guest feature, be it an introduction to your tool, updates or upcoming features or even an opinion about the current state of genomics research and data, please write us at wlathe AT openhelix DOT com. We would love to put you in the queue for the next guest post.

Our first guest post next Tuesday will be from Inna Dubchak , principal investigator at the LBNL/JGI group, developers of the VISTA comparative genomics resource (who sponsors a tutorial, free to the users). She’ll discuss some new tools at VISTA and give you a quick preview of some new upcoming features.

Tip of the Week: Sharing your analysis process

galaxyworkflow_thWe’ve introduced Galaxy (http://www.usegalaxy.org) before in the Tip of the Week section, have showed you one thing useful you could do with it, and now we also have a free tutorial and training materials that introduce you to the basic use of the tool. In today’s tip of the week, I’m going to show you workflows. Workflows was in beta until recently, so it isn’t in the first version of our tutorial (though it will be in the second). It’s a great feature, so I wanted to introduce it here. Workflows allows you to set up an automated process that takes your data through a preset series of manipulation and analysis steps. This can be very useful if there is a process you are doing a lot and you don’t want to have to do each step every time, or if you create a analysis process you’d like to share with a colleague. (and I’d like to point out that Galaxy has a good number of other short screencasts of tasks you might want to check out after doing the tutorial )

What's your problem? Open Thread

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to askq_mark2.jpg questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

What's your problem? Open Thread

q_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

What's Your Problem? Open Thread

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to askq_mark2.jpg questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

What’s Your Problem? Open Thread

q_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

{I’m closing comments here since a fresh thread is up–Mary}