Mary

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OpenHelix
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  • March 26, 2015
  • 09:41 AM
  • 11 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
  • 40 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
  • 75 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
  • 77 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
  • 69 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
  • 122 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
  • 124 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 effectively, and it’s time to include this in our Video Tips of the Week.... Read more »

  • February 11, 2015
  • 09:38 AM
  • 129 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
  • 97 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
  • 116 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
  • 72 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
  • 145 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
  • 167 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
  • 257 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
  • 185 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
  • 177 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 »

  • December 11, 2014
  • 09:39 AM
  • 169 views

What’s the Answer? (tidy data format)

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 »

Wickham Hadley Wickham. (2014) Tidy Data. Journal of Statistical Software, 59(10). info:other/JSSOBK:v59i10

  • December 10, 2014
  • 09:38 AM
  • 203 views

Video Tip of the Week: “Virtually Immune” computational immune system modeling

by Mary in OpenHelix

This week’s video tip of the week is the next in a series. It began when I took a look at GeneFriends, and their option to output the data for use in BioLayout Express3D. So of course we had to then take a look at BioLayout. While I was exploring BioLayout, I came across Virtually […]... Read more »

  • December 8, 2014
  • 10:47 AM
  • 151 views

Oxford plots from the gibbon genome paper

by Mary in OpenHelix

A while back I talked about the software in the gibbon genome paper. I went through to try to pull out as much of the software as I could as sort of a catalog of a representative genome project. Of course, there was a lot in there. Some of it, though, consisted of unpublished code. […]... Read more »

Carbone Lucia, R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: http://dx.doi.org/10.1038/nature13679  

  • December 3, 2014
  • 09:38 AM
  • 145 views

Video Tip of the Week: BioLayout Express3D for network visualizations

by Mary in OpenHelix

My previous Video Tip of the Week highlighted the GeneFriends tool. With GeneFriends you can search for co-expression of genes in RNA-seq data sets. But you can take these results further and visualize them with the BioLayout Express3D tool, so I wanted to bring more details about BioLayout in this tip since we haven’t covered […]... Read more »

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