Mary

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OpenHelix
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  • April 27, 2015
  • 08:34 AM
  • 23 views

Phytozome notice, new and improved v10 coming soon

by Mary in OpenHelix

This announcement came out while I was at a conference last week–but I wanted to pass it along. This appears to be a big change in the way Phytozome works. And there will be down-time before it rolls out, starting May 1. I like to post major announcements from mailing lists because I know everyone […]... Read more »

Goodstein D. M., R. Howson, R. Neupane, R. D. Hayes, J. Fazo, T. Mitros, W. Dirks, U. Hellsten, N. Putnam, & D. S. Rokhsar. (2011) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1). DOI: http://dx.doi.org/10.1093/nar/gkr944  

  • April 22, 2015
  • 08:26 AM
  • 55 views

Video Tip of the Week: TargetMine, Data Warehouse for Drug Discovery

by Mary in OpenHelix

Browsing around genomic regions, layering on lots of associated data, and beginning to explore new data types I might come across are things that really fire up my brain. For me, visualization is key to forming new ideas about the relationships between genomic features and patterns of data. But frequently I want to take this […]... Read more »

Kalderimis A., D. Butano, S. Contrino, M. Lyne, J. Heimbach, F. Hu, R. Smith, R.  t pan, J. Sullivan, & G. Micklem. (2014) InterMine: extensive web services for modern biology. Nucleic Acids Research, 42(W1). DOI: http://dx.doi.org/10.1093/nar/gku301  

  • April 15, 2015
  • 09:35 AM
  • 77 views

Video Tip of the Week: Viewing Amino Acid info in the UCSC Genome Browser

by Mary in OpenHelix

We’ve been doing training on the UCSC Genome Browser for over 10 years now. We’ve seen it grow from just a few genomes and a few tracks to the enormous trove of information it is today. In fact, one of the toughest things about training is how to balance all the new information and features […]... Read more »

Rosenbloom K. R., G. P. Barber, J. Casper, H. Clawson, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler, & R. A. Harte. (2014) The UCSC Genome Browser database: 2015 update. Nucleic Acids Research, 43(D1). DOI: http://dx.doi.org/10.1093/nar/gku1177  

  • April 1, 2015
  • 09:39 AM
  • 92 views

Video Tip of the Week: The New OpenHelix Interface

by Mary in OpenHelix

Generally we like to highlight new features and new tools from bioinformatics software providers. But this week we wanted to introduce some new features of our own OpenHelix site. If you’ve been using the site for a while, you will have noticed that recently we rolled out some changes. All the same tutorial materials and […]... Read more »

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

  • March 26, 2015
  • 09:41 AM
  • 85 views

What’s the Answer? (alignment editors)

by Mary in OpenHelix

This week’s highlighted question is from the Bioinformatics discussion area at Reddit. There are a range of topics discussed in that subreddit, and some of the tool-specific ones are very helpful in learning about new software. What are some of the best multiple alignment editors that allow for manual editing? Cross-platform/open-source would be preferred. –AtlasAnimated […]... Read more »

  • March 25, 2015
  • 09:38 AM
  • 103 views

Video Tip of the Week: Protein structure information for public outreach. Really.

by Mary in OpenHelix

This week’s tip isn’t about a specific tool–but a really interesting look at how a tool was used in the context of some general public outreach messaging. Recently I posted about Aquaria, a new tool available to let biologists explore protein structures, mutations, and domains in user-friendly ways. But an interesting example of how the […]... Read more »

O'Donoghue Seán I, Maria Kalemanov, Christian Stolte, Benjamin Wellmann, Vivian Ho, Manfred Roos, Nelson Perdigão, Fabian A Buske, Julian Heinrich, & Burkhard Rost. (2015) Aquaria: simplifying discovery and insight from protein structures. Nature Methods, 12(2), 98-99. DOI: http://dx.doi.org/10.1038/nmeth.3258  

  • March 18, 2015
  • 09:36 AM
  • 126 views

Video Tip of the Week: Designing proteins, using Rosetta

by Mary in OpenHelix

As often happens, last week’s tip on visualizing structures led me to some more reading and thinking about creating protein structures. And although it’s important for biologists to be able to use more of the information about protein structures and variations in their work from tools like Aquaria or PDB, it’s also important for some […]... Read more »

Kuroda D., M. P. Jacobson, & H. Nakamura. (2012) Computer-aided antibody design. Protein Engineering Design and Selection, 25(10), 507-522. DOI: http://dx.doi.org/10.1093/protein/gzs024  

  • March 11, 2015
  • 09:42 AM
  • 118 views

Video Tip of the Week: Aquaria, streamlined access to protein structures for biologists

by Mary in OpenHelix

This week’s Video Tip of the Week is Aquaria, a new resource for exploring protein structures, mutations, and similarities to other proteins. It’s a very well-designed and interactive experience for end users. It is aimed largely at biologists who could benefit from exploring the structural details of their proteins of interest, but are daunted by […]... Read more »

O'Donoghue Seán I, Maria Kalemanov, Christian Stolte, Benjamin Wellmann, Vivian Ho, Manfred Roos, Nelson Perdigão, Fabian A Buske, Julian Heinrich, & Burkhard Rost. (2015) Aquaria: simplifying discovery and insight from protein structures. Nature Methods, 12(2), 98-99. DOI: http://dx.doi.org/10.1038/nmeth.3258  

  • March 4, 2015
  • 09:41 AM
  • 105 views

Video Tip of the Week: Beacon, to locate genome variants of potential clinical significance

by Mary in OpenHelix

This week’s Video Tip of the Week follows on last week’s chatter about the Internet of DNA. As I mentioned then, the Beacon tool we touched on was going to get more coverage. So this week’s video is provided by the Beacon team, part of the larger Global Alliance for Genomics and Health project (GA4GH). […]... Read more »

Nguyen Ngan, Daniel R. Zerbino, Brian Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, & Benedict Paten. (2015) Building a Pan-Genome Reference for a Population. Journal of Computational Biology, 2147483647. DOI: http://dx.doi.org/10.1089/cmb.2014.0146  

  • February 25, 2015
  • 09:41 AM
  • 154 views

Video Tip of the Week: CRISPRdirect for editing tools and off-target information

by Mary in OpenHelix

Genome editing strategies are certainly a hot topic of late. We were astonished at the traffic that the animation of the CRISPR/Cas-9 process recently drew to the blog. There’s a huge amount of potential for novel types of studies and interventions in human disease situations–but I’m already seeing applications in agriculture coming along. There’s an […]... Read more »

  • February 20, 2015
  • 10:52 AM
  • 164 views

Video Tip of the Week: RStudio as an interface for using R

by Mary in OpenHelix

Although typically we focus on databases and algorithms in use in bioinformatics and genomics, there are some other tools that support this work that are crucial as well. The statistical software and computing tools associated with R fall into this category. Increasingly RStudio is being adopted by folks in genomics, and although we talked about R in the past, I hadn’t highlighted the RStudio interface before. But this really lowered the barrier to entry, and has changed the way to use R e........ Read more »

  • February 11, 2015
  • 09:38 AM
  • 170 views

Video Tip of the Week: IntOGen, for Integrative OncoGenomics

by Mary in OpenHelix

When I’m looking for upcoming Tips of the Week, frequently one tool or paper will lead me to looking at other related tools in that sphere. Last week’s tip on COSMIC got me looking through cancer genomics resources, and one of the others that I came across is IntOGen, “Integrative Onco Genomics”. Their Nature Methods […]... Read more »

Gonzalez-Perez Abel, Jordi Deu-Pons, David Tamborero, Michael P Schroeder, Alba Jene-Sanz, Alberto Santos, & Nuria Lopez-Bigas. (2013) IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods, 10(11), 1081-1082. DOI: http://dx.doi.org/10.1038/nmeth.2642  

  • February 4, 2015
  • 09:38 AM
  • 127 views

Video Tip of the Week: COSMIC, Catalogue Of Somatic Mutations In Cancer

by Mary in OpenHelix

When we do workshops at medical centers, one of the most common questions I get is about locating good resources for cancer data. And we’ve talked about some of the large projects, like the ICGC. We’ve talked about ways to stratify data sets, and one example of this was in cancer, using data from The […]... Read more »

Forbes S. A., P. Gunasekaran, K. Leung, N. Bindal, H. Boutselakis, M. Ding, S. Bamford, C. Cole, S. Ward, & C. Y. Kok. (2014) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Research, 43(D1). DOI: http://dx.doi.org/10.1093/nar/gku1075  

  • January 28, 2015
  • 08:38 AM
  • 159 views

Video Tip of the Week: Helium plant pedigree software, because “Plants are weird.”

by Mary in OpenHelix

A lot of people find our blog by searching for “pedigree” tools. We’ve covered them in the past, and we’ve got some training on the Madeline 2.0 web tools that we like. We have groused about the fact that some pedigree tools do not accommodate same-sex families. Largely focused on human relationships, there are a […]... Read more »

Shaw Paul D, Jessie Kennedy, Iain Milne, & David F Marshall. (2014) Helium: visualization of large scale plant pedigrees. BMC Bioinformatics, 15(1), 259. DOI: http://dx.doi.org/10.1186/1471-2105-15-259  

  • January 21, 2015
  • 09:07 AM
  • 97 views

Video Tip of the Week: GWATCH, for flying over chromosomes

by Mary in OpenHelix

Ok, so it’s not *just* for flying over chromosomes. There’s more to it, of course. But that’s the part of GWATCH (Genome-Wide Association Tracks Chromosome Highway) that caught my attention. I’m always looking for different ideas and strategies to visualize data, and this was the first time I drove along the whole length of a […]... Read more »

Svitin Anton, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer Troyer, Sher Hendrickson, & Holli Dilks. (2014) GWATCH: a web platform for automated gene association discovery analysis. GigaScience, 3(1), 18. DOI: http://dx.doi.org/10.1186/2047-217x-3-18  

  • January 14, 2015
  • 09:39 AM
  • 175 views

Video Tip of the Week: Genome assemblers and #Docker

by Mary in OpenHelix

Last fall there was a tip I did on Docker, which was starting to pick up a lot of chatter around the genoscenti. It was starting to look like a good solution for some of the problems of reproducibility and re-use of software in genomics–containerize it. Box it up, hand it off. There’s certainly a […]... Read more »

Veras Adonney, Vasco Azevedo, Artur Silva, Rommel Ramos, Institute of Biological Sciences, Federal University Pará, Belém, Pará, & Brazil. (2013) AutoAssemblyD: a graphical user interface system for several genome assemblers. Bioinformation, 9(16), 840-841. DOI: http://dx.doi.org/10.6026/97320630009840  

Hildebrandt A. K., N. M. Fischer, L. de la Garza, J. Kruger, S. Nickels, M. Rottig, C. Scharfe, M. Schumann, P. Thiel, & H.-P. Lenhof. (2014) ballaxy: web services for structural bioinformatics. Bioinformatics, 31(1), 121-122. DOI: http://dx.doi.org/10.1093/bioinformatics/btu574  

  • January 7, 2015
  • 09:46 AM
  • 195 views

Video Tip of the Week: PhosphoSitePlus, protein post-translational modifications

by Mary in OpenHelix

Nucleotide sequence data and analysis commands the bulk of my attention on most days. But certainly post-translational modification of proteins has a lot of influence on the ultimate function (or dysfunction, in some cases) of the genes in play in a given situation. A recent paper reminded me of a resource that I’ve known about […]... Read more »

  • December 30, 2014
  • 12:04 PM
  • 290 views

Margaret Oakley Dayhoff, going on #ThatOtherShirt.

by Mary in OpenHelix

I’ve been a fan of Margaret Oakley Dayhoff for a long time. One of the most popular posts on this blog is the one linked in this tweet below. I can tell when students have been assigned a project to read up on her, because suddenly I see an influx of hits to the page. […]... Read more »

  • December 18, 2014
  • 09:36 AM
  • 210 views

What’s the Answer? (FANTOM5 promoter atlas)

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 »

Forrest Alistair R. R., Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, & Robin Andersson. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493), 462-470. DOI: http://dx.doi.org/10.1038/nature13182  

Severin Jessica, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, Nicolas Bertin, & Alistair R R Forrest. (2014) Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32(3), 217-219. DOI: http://dx.doi.org/10.1038/nbt.2840  

  • December 17, 2014
  • 09:38 AM
  • 202 views

Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks

by Mary in OpenHelix

This week’s video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week’s tool is the final piece that you need to know about if you want to create the kind of […]... Read more »

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