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On the OpenHelix blog you will find a genomics resources news portal with daily postings about genomics and bioinformatics resources, genomics news and research, science and more. Our goal is to keep you, the researcher, informed about the overwhelming amount of genomics data out there and how to access it through the tools, databases and resources that are publicly available to you.

Mary
125 posts

Trey
4 posts

Jennifer
35 posts

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  • April 23, 2014
  • 09:36 AM
  • 2 views

Video Tip of the Week: Atlas of Cancer Signaling Networks

by Mary in OpenHelix

Last week I highlighted a software tool that lets you customize maps of molecular interactions, and navigate around at various resolutions to explore. It’s called NaviCell, and it seems to offer a lot of opportunity for folks to develop helpful maps related to their research. This week I’m going to note that this same team […]... Read more »

Kuperstein Inna, Cohen David PA, Pook Stuart, Viara Eric, Calzone Laurence, Barillot Emmanuel, & Zinovyev Andrei. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(1), 100. DOI: 10.1186/1752-0509-7-100  

  • April 17, 2014
  • 09:39 AM
  • 68 views

What’s the Answer? (new Biostars interface)

by Mary in OpenHelix

BioStars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here […]... Read more »

Parnell Laurence D., Lindenbaum Pierre, Shameer Khader, Dall'Olio Giovanni Marco, Swan Daniel C., Jensen Lars Juhl, Cockell Simon J., Pedersen Brent S., Mangan Mary E., & Miller Christopher A. (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216.g002  

  • April 16, 2014
  • 09:37 AM
  • 73 views

Video Tip of the Week: NaviCell for custom interaction maps for systems biology

by Mary in OpenHelix

The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a […]... Read more »

Kuperstein Inna, Cohen David PA, Pook Stuart, Viara Eric, Calzone Laurence, Barillot Emmanuel, & Zinovyev Andrei. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(1), 100. DOI: 10.1186/1752-0509-7-100  

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N., & Kitano H. (2008) CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE, 96(8), 1254-1265. DOI: 10.1109/JPROC.2008.925458  

  • April 10, 2014
  • 09:14 AM
  • 146 views

What’s The Answer? (1000 Genomes signatures)

by Mary in OpenHelix

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here […]... Read more »

Pybus M., Dall'Olio G. M., Luisi P., Uzkudun M., Carreno-Torres A., Pavlidis P., Laayouni H., Bertranpetit J., & Engelken J. (2013) 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1188  

  • April 9, 2014
  • 10:40 AM
  • 54 views

Video Tip of the Week: list of genes associated with a disease

by Trey in OpenHelix

I am currently in Puerto Varas, Chile at an EMBO genomics workshop. The workshop is mainly for grad students and the instructors are, for the most part, alumni of the Bork group. I gave a tutorial on genomics databases. Anyway, the last two days of the workshop is a challenge, in teams of 3-4 advised […]... Read more »

Laulederkind S. J. F., Hayman G. T., Wang S.-J., Smith J. R., Lowry T. F., Nigam R., Petri V., de Pons J., Dwinell M. R., & Shimoyama M. (2013) The Rat Genome Database 2013--data, tools and users. Briefings in Bioinformatics, 14(4), 520-526. DOI: 10.1093/bib/bbt007  

  • April 2, 2014
  • 09:37 AM
  • 83 views

Video Tip of the Week: EuPathDB

by Mary in OpenHelix

I love pathogens and parasites. Really, I do. I mean–not up very close. But their astonishing range and cleverness often earns my respect. How these small organisms can wreak havoc on larger systems, inveigle the larger organisms to fly, carry, or ship them around during appropriate points in their life cycle, and to cloak themselves […]... Read more »

Aurrecoechea C., Brestelli J., Brunk B. P., Fischer S., Gajria B., Gao X., Gingle A., Grant G., Harb O. S., & Heiges M. (2009) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp941  

  • March 24, 2014
  • 05:29 PM
  • 46 views

GenoCAD webinar this Thursday, March 27

by Mary in OpenHelix

Although it’s already posted in our news feed, I just wanted to add a reminder about our upcoming webinar on GenoCAD: open-source computer-assisted design software for synthetic biology. You can see the time and registration details here: Free “Introduction to GenoCAD” Webinar presented March 27th If you want to download the slides beforehand (so you […]... Read more »

  • March 19, 2014
  • 09:38 AM
  • 89 views

Video Tip of the Week: ICGC portal for cancer genomics

by Mary in OpenHelix

A question at Biostar about cancer “gene sets” recently got me looking at one of my favorite data sources again–the ICGC, International Cancer Genome Consortium, and their data portal. Previous posts we’ve done were based on their legacy portal (which is still available on their site). They changed things up a bit with a release […]... Read more »

Hudson (Chairperson) Thomas J., Anderson Warwick, Aretz Axel, Barker Anna D., Bell Cindy, Bernabé Rosa R., Bhan M. K., Calvo Fabien, Eerola Iiro, & Gerhard Daniela S. (2010) International network of cancer genome projects. Nature, 464(7291), 993-998. DOI: 10.1038/nature08987  

Alexandrov Ludmil B., Nik-Zainal Serena, Wedge David C., Aparicio Samuel A. J. R., Behjati Sam, Biankin Andrew V., Bignell Graham R., Bolli Niccolò, Borg Ake, & Børresen-Dale Anne-Lise. (2013) Signatures of mutational processes in human cancer. Nature, 500(7463), 415-421. DOI: 10.1038/nature12477  

Gonzalez-Perez Abel, Mustonen Ville, Reva Boris, Ritchie Graham R S, Creixell Pau, Karchin Rachel, Vazquez Miguel, Fink J Lynn, Kassahn Karin S, & Pearson John V. (2013) Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods, 10(8), 723-729. DOI: 10.1038/nmeth.2562  

  • March 12, 2014
  • 10:30 AM
  • 107 views

Video Tip of the Week: JANE, comparing phylogenies

by Trey in OpenHelix

Unable to display content. Adobe Flash is required. When I was doing my Ph.D. in the ancient days of the Sanger Method sequencing and reading in the results with one hand on the keyboard and reading the GATCs on the read (and going to the lab in the snow uphill both ways), my purpose for […]... Read more »

Conow, C., Fielder, D., Ovadia, Y., & Libeskind-Hadas, R. (2010) Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology, 5(1), 16. DOI: 10.1186/1748-7188-5-16  

  • March 10, 2014
  • 10:02 AM
  • 124 views

New UCSC Genome Browser for the newest human genome assembly

by Mary in OpenHelix

Most folks who read this blog will be aware that a new human genome assembly has been completed, released, and is available for anyone to obtain. One of my favorite overviews of that new version can be found in this readable piece at Bio-IT World: Deanna Church on the Reference Genome Past, Present and Future. […]... Read more »

Karolchik D., Barber G. P., Casper J., Clawson H., Cline M. S., Diekhans M., Dreszer T. R., Fujita P. A., Guruvadoo L., & Haeussler M. (2013) The UCSC Genome Browser database: 2014 update. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1168  

  • March 5, 2014
  • 09:40 AM
  • 108 views

Video Tip of the Week: Introduction to IGB Genome Browser

by Mary in OpenHelix

Last fall I noticed an announcement at Biostar about an upcoming webinar that would illustrate some new features in the IGB browser. And at the time I highlighted some of their materials as our video tip that week.  So for more details you can check out that overview. But recently I was told that their […]... Read more »

  • February 26, 2014
  • 09:38 AM
  • 142 views

Video Tip of the Week: Ambiscript Mosaic for visualizing nucleotide motifs

by Mary in OpenHelix

One of the topics I keep an eye on is visualization of various types of genomics data, and I’m always interested in new tools for graphical representations. In the past some of our most popular posts have been tools that aren’t heavy-lifting analysis types of tools–but better ways to visualize and explore data, or different […]... Read more »

  • February 19, 2014
  • 09:35 AM
  • 112 views

Video Tip of the Week: Centralized Model Organism Database (CMOD)

by Mary in OpenHelix

This week’s Tip of the Week is a bit different. The database resource that’s the focus of this piece doesn’t exist yet. Parts of it do, but there’s a ways to go before we actually have a Centralized Model Organism Database (CMOD). The ideas that Andrew Su offers for CMOD in this talk are ones […]... Read more »

Howe Doug, Costanzo Maria, Fey Petra, Gojobori Takashi, Hannick Linda, Hide Winston, Hill David P., Kania Renate, Schaeffer Mary, & St Pierre Susan. (2008) Big data: The future of biocuration. Nature, 455(7209), 47-50. DOI: 10.1038/455047a  

  • February 12, 2014
  • 04:03 PM
  • 109 views

Video Tip of the Week: MetaPhlAn and Galaxy

by Trey in OpenHelix

CPB Using Galaxy 2 from Galaxy Project on Vimeo. for loading and using datatypes and  the OpenHelix Galaxy tutorial for getting familiar with Galaxy interface and usage. Metagenomics analysis can be a bit daunting at times, but there are a good number of tools out there to assist a researcher in analysis.  Integrated Microbial Genomes at […]... Read more »

Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson . (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods, 811-814. info:/doi:10.1038/nmeth.2066

  • January 29, 2014
  • 09:36 AM
  • 182 views

Video Tip of the Week: NCBI Sequence Viewer PDF export

by Mary in OpenHelix

A couple of weeks back we did a workshop on the UCSC Genome Browser, and I was asked a question we see pretty frequently: Is there a way to export the browser view that you selected with specific tracks, filters, regions, etc? People may want to have a record of their customized view in a […]... Read more »

Karolchik D., Barber G. P., Casper J., Clawson H., Cline M. S., Diekhans M., Dreszer T. R., Fujita P. A., Guruvadoo L., & Haeussler M. (2013) The UCSC Genome Browser database: 2014 update. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1168  

Acland A., Agarwala R., Barrett T., Beck J., Benson D. A., Bollin C., Bolton E., Bryant S. H., Canese K., & Church D. M. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1146  

  • January 22, 2014
  • 09:35 AM
  • 157 views

Video Tip of the Week: StratomeX

by Mary in OpenHelix

Last week I talked about some of the terrific visualization tools from the Caleydo team, the ones that are focused on looking at pathway data. There’s another tool that I learned about in their newsletter that offers another type of visualization, which you can also supplement with pathway data. StratomeX offers a look at comparisons […]... Read more »

Schroeder Michael P, Gonzalez-Perez Abel, & Lopez-Bigas Nuria. (2013) Visualizing multidimensional cancer genomics data. Genome Medicine, 5(1), 9. DOI: 10.1186/gm413  

  • January 15, 2014
  • 08:05 AM
  • 148 views

Video Tip of the Week: Entourage and enRoute from the Caleydo team

by Mary in OpenHelix

Have you dreamed of looking at genomic pathway data, with experimental information aligned with known pathway details, and wandering easily from one pathway node to another as you consider the implication of increased/decreased gene expression, or potential copy number variations? Easily hopping to related pathways to keep looking? Yeah–me too, for years .  If this […]... Read more »

  • December 18, 2013
  • 09:33 AM
  • 143 views

Video tip of the Week: CodersCrowd

by Mary in OpenHelix

Over the last few months I’ve been following the progress of a project called CodersCrowd, a social-media-crowdsourcing-coding-project site. The first musings I saw about it came from the bioinformatiscenti via twitter and Biostar:  News: #Bioinformatics Crowdcoding.  They were interested, and “cautiously optimistic” about it. But I was waiting to be sure it launched to highlight […]... Read more »

Parnell Laurence D., Lindenbaum Pierre, Shameer Khader, Dall'Olio Giovanni Marco, Swan Daniel C., Jensen Lars Juhl, Cockell Simon J., Pedersen Brent S., Mangan Mary E., & Miller Christopher A. (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216.g002  

  • December 11, 2013
  • 09:36 AM
  • 337 views

Video Tip of the Week: UCSC Track Hubs

by Mary in OpenHelix

Over the years we’ve seen some real shifts in the needs of the trainees in our UCSC Genome Browser workshops. At first, people just needed access to the reference genome and the data that was available (and boy, has that changed over the years–time travel back with this post!). But as researchers around the world […]... Read more »

Raney B. J., Dreszer T. R., Barber G. P., Clawson H., Fujita P. A., Wang T., Nguyen N., Paten B., Zweig A. S., & Karolchik D. (2013) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. DOI: 10.1093/bioinformatics/btt637  

Karolchik D., Barber G. P., Casper J., Clawson H., Cline M. S., Diekhans M., Dreszer T. R., Fujita P. A., Guruvadoo L., & Haeussler M. (2013) The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. DOI: 10.1093/nar/gkt1168  

  • December 4, 2013
  • 12:13 PM
  • 226 views

Tip of the Week: Creating an Electronic Informed Consent

by Trey in OpenHelix

Informed consent has been a foundation of research, and especially genetics research, in that last few decades though it’s taken quite some time to right past wrongs. And with genomics research and personal genomics generating huge amounts of data, informed consent becomes both more important and more complex. The National Human Genome Research Institute has […]... Read more »

Charles N Rotimi and Patricia A Marshall. (2010) Tailoring the process of informed consent in genetic and genomic research. Genome Medicine, 2(3). info:/doi:10.1186/gm141

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