Mary

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OpenHelix
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  • April 16, 2014
  • 09:37 AM
  • 14 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
  • 134 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 2, 2014
  • 09:37 AM
  • 75 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
  • 41 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
  • 80 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 10, 2014
  • 10:02 AM
  • 116 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
  • 103 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
  • 134 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
  • 108 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  

  • January 29, 2014
  • 09:36 AM
  • 136 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
  • 148 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
  • 141 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
  • 140 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
  • 328 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  

  • November 20, 2013
  • 09:39 AM
  • 170 views

Video Tip of the Week: IGB, Integrated Genome Browser

by Mary in OpenHelix

Recently in a paper we are working on we were asked to cover a bit more about various styles or types of genome browsers that are available. And the timing was perfect, because I had just revisited the information about IGB (Ig-bee) in their recent webinar series. Announced on Biostar recently was this nice introduction […]... Read more »

  • November 13, 2013
  • 09:47 AM
  • 205 views

Video Tip of the Week: Advanced Topics in GenoCAD

by Mary in OpenHelix

Recently we announced our newest training materials on GenoCAD. The introductory tutorial provides a great foundation for understanding the features that are available and how it could help you in the lab. But for those folks who want to take their design skills further–now you can use the GenoCAD Advanced Topics materials to do so. […]... Read more »

  • November 11, 2013
  • 10:02 AM
  • 198 views

Antique (or maybe “classic”) UCSC Genome Browsers retired

by Mary in OpenHelix

Everyone is pretty comfortable with the concept of the non-standard but commonly used dog-years as a way to compare life spans to humans. Car enthusiasts have a taxonomy for the ages of vehicles. But I’ve been sitting here wondering what the genome-browser-years scale should be. I’ve been thinking about it because of the recent announcement […]... Read more »

Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., & Haussler D. (2002) The Human Genome Browser at UCSC. Genome Res., 996-1006. DOI: 10.1101/gr.229102  

  • October 30, 2013
  • 09:33 AM
  • 244 views

Video Tip of the Week: VectorEditor

by Mary in OpenHelix

For this week’s video tip of the week, I’ll give you a quick tour of the VectorEditor software. It’s a handy tool that you can install locally, or use on the web, to edit and display features of your DNA constructs. It’s got all of the key features that you might want–annotations, graphics, sequence, restriction […]... Read more »

  • October 23, 2013
  • 09:33 AM
  • 176 views

Video Tip of the Week: PATRIC Protein Family Sorter

by Mary in OpenHelix

So just last night my twitter feed was abuzz with bacterial infection drama. The Frontline PBS show was doing a whole episode called “Hunting the Nightmare Bacteria” and based on the chatter I’d say they struck a nerve. Our antibiotic arsenal is failing us, and it’s crucial to figure out new ways to battle these […]... Read more »

Gillespie J. J., Wattam A. R., Cammer S. A., Gabbard J. L., Shukla M. P., Dalay O., Driscoll T., Hix D., Mane S. P., & Mao C. (2011) PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species. Infection and Immunity, 79(11), 4286-4298. DOI: 10.1128/IAI.00207-11  

  • October 16, 2013
  • 09:37 AM
  • 161 views

Video Tip of the Week: Mobile-device enabled tutorial suites

by Mary in OpenHelix

For decade now we’ve been offering our video tutorial suites to help people learn how to use bioinformatics resources. We’ve used a couple of delivery platforms, and we’ve changed the website a few times. But we also know that people like consistency with software, and if there are going to be major changes to the […]... Read more »

Williams J. M., Mangan M. E., Perreault-Micale C., Lathe S., Sirohi N., & Lathe W. C. (2010) OpenHelix: bioinformatics education outside of a different box. Briefings in Bioinformatics, 11(6), 598-609. DOI: 10.1093/bib/bbq026  

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