Tag Archives: Argo

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


Can you spare a genome browser?

Recently I’ve been coming across more and more requests and need for genome annotation and visualization software. Genomes are being completed left and right and researchers need ways to browse and annotate these genomes. There are a lot of tools out there. This post is a quick attempt to start listing those. It is not exhaustive right now, right now there are the ones off the top of my head and those focused a bit on visualization (though there is annotation). I plan to expand this list (have any to suggest) and enhance it with more descriptions as time goes forward. Probably make it a page if it becomes useful enough. I’m not listing databases (such as UCSC Genome Browser, RGD, Ensembl, Flybase, but rather software that researchers can use to create such browsable genomes). So, here we go…

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