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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
201 posts

Trey
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Jennifer
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  • July 1, 2015
  • 09:39 AM
  • 49 views

Video Tip of the Week: MorphoGraphX, morphogenesis in 4D

by Mary in OpenHelix

This week’s Video Tip of the Week covers a different aspect of bioinformatics than some of our other tips. But having been trained as a cell biologist, I do consider imaging software as an important part of the crucial software ecosystem. Also, since it’s a holiday week and traffic may be light in the US, […]... Read more »

Barbier de Reuille, P., Routier-Kierzkowska, A., Kierzkowski, D., Bassel, G., Schüpbach, T., Tauriello, G., Bajpai, N., Strauss, S., Weber, A., Kiss, A.... (2015) MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife. DOI: 10.7554/eLife.05864  

  • June 24, 2015
  • 10:30 AM
  • 71 views

Video Tip of the Week: handy way to make citations quickly

by Mary in OpenHelix

This is not a typical tip–where we explore the features and details of bioinformatics tools. But it’s one of those handy little features that may make your life easier. It’s made mine better lately. I had been using the ScienceSeeker citation generator system for creating citations that would then aggregate to either ScienceSeeker or ResearchBlogging. But ScienceSeeker’s model recently changed. And ResearchBlogging’s support and stability is…well, uneven.... Read more »

  • June 17, 2015
  • 09:38 AM
  • 29 views

Video Tip of the Week: ZBrowse for GWAS viewing and exploration

by Mary in OpenHelix

Maybe you’ve heard of the others. ABrowse. BBrowse. CBrowse. [you get the idea] GBrowse has been widely adopted. JBrowse is picking up steam. Into the orderly arrangement we now throw ZBrowse: a new way to look at genome-wide association study data. Sharing and chatter about ZBrowse for viewing GWAS was abundant when the paper was […]... Read more »

  • June 11, 2015
  • 09:35 AM
  • 136 views

What’s the Answer? (pan-genome graphs)

by Mary in OpenHelix

This weeks highlighted discussion is the problem of pan-genome graphs, which are ways to represent the variation we find in genomes instead of a linear reference sequence view. I was really struggling with these concepts until I heard a talk at the #TRICON meeting recently. David Haussler had some really helpful visuals. I don’t have […]... Read more »

Benedict Paten, Adam Novak, & David Haussler. (2014) Mapping to a Reference Genome Structure. arXiv.org. arXiv: 1404.5010v1

Nguyen, N., Hickey, G., Zerbino, D., Raney, B., Earl, D., Armstrong, J., Kent, W., Haussler, D., & Paten, B. (2015) Building a Pan-Genome Reference for a Population. Journal of Computational Biology, 22(5), 387-401. DOI: 10.1089/cmb.2014.0146  

  • June 10, 2015
  • 09:36 AM
  • 106 views

Video Tip of the Week: GenomeConnect, the ClinGen piece for patients

by Mary in OpenHelix

GenomeConnect is part of the larger ClinGen effort that I began to discuss last week, but this aspect is specifically a portal for patients who have (or may get) genetic testing results of various types. The ClinGen team will use this interface to capture the testing data–the genotypes, and the health history, or phenotypes, and […]... Read more »

Rehm, H., Berg, J., Brooks, L., Bustamante, C., Evans, J., Landrum, M., Ledbetter, D., Maglott, D., Martin, C., Nussbaum, R.... (2015) ClinGen — The Clinical Genome Resource. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMsr1406261  

  • June 3, 2015
  • 09:38 AM
  • 150 views

Video Tip of the Week: ClinGen, The Clinical Genome Resource

by Mary in OpenHelix

The sequence data tsunami begins to crash into the shore, at the feet of clinicians and patients who want answers and treatment directions. But sometimes the tsunami is washing in debris. As the amount of sequence and variation information grows, some of it comes without clear evaluations of the impacts. Some of it comes with […]... Read more »

Rehm, H., Berg, J., Brooks, L., Bustamante, C., Evans, J., Landrum, M., Ledbetter, D., Maglott, D., Martin, C., Nussbaum, R.... (2015) ClinGen — The Clinical Genome Resource. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMsr1406261  

  • May 27, 2015
  • 09:40 AM
  • 148 views

Video Tip of the Week: PANDA (Pathway AND Annotation) Explorer for lists of genes

by Mary in OpenHelix

This week’s Video Tip of the Week demonstrates PANDA, a tool for generating and examining annotations that are available for a list of genes, and evaluating them in the context of pathways. Two great tastes that taste great together, you know? So have a look at how PANDA can help you and your team to […]... Read more »

  • May 20, 2015
  • 09:34 AM
  • 173 views

Video Tip of the Week: NCBI Tree Viewer

by Mary in OpenHelix

The helpful folks at NCBI have been ramping up their outreach. I’ve been watching a lot of their webinars, and they are trying different styles. The more traditional ones that are about the length of a seminar, and lately shorter quick-hit types of things. Both of them are valuable. Some topics need a good foundational […]... Read more »

  • May 14, 2015
  • 09:39 AM
  • 145 views

What’s The Answer? (brain connectome)

by Mary in OpenHelix

This week’s highlighted item lets you find answers in brains. What do the brain connections look like in 3D? I love 3D brain maps–not in a zombie manner, just in an astonishing complexity manner. And although this is a different type of computational resource than we usually explore, I thought it was interesting. Biostars is […]... Read more »

Szalkai, B., Kerepesi, C., Varga, B., & Grolmusz, V. (2015) The Budapest Reference Connectome Server v2.0. Neuroscience Letters, 60-62. DOI: 10.1016/j.neulet.2015.03.071  

  • May 13, 2015
  • 09:43 AM
  • 108 views

Video Tip of the Week: PhenogramViz for evaluating phenotypes and CNVs

by Mary in OpenHelix

As I’ve mentioned before, once I start looking over some new tools I’m often led to others in the same arena that offer related but different features. That’s what happened when I looked at the Proband iPad app for human pedigrees. I noted that they are using important community standards, and I decided to follow […]... Read more »

Kohler, S., Doelken, S., Mungall, C., Bauer, S., Firth, H., Bailleul-Forestier, I., Black, G., Brown, D., Brudno, M., Campbell, J.... (2013) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1026  

Köhler Sebastian, Doelken Sandra C, Ruef Barbara J, Bauer Sebastian, Washington Nicole, Westerfield Monte, Gkoutos George, Schofield Paul, Smedley Damian, & Lewis Suzanna E. (2013) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Research. PMID: 24358873  

Kohler, S., Schoeneberg, U., Czeschik, J., Doelken, S., Hehir-Kwa, J., Ibn-Salem, J., Mungall, C., Smedley, D., Haendel, M., & Robinson, P. (2014) Clinical interpretation of CNVs with cross-species phenotype data. Journal of Medical Genetics, 51(11), 766-772. DOI: 10.1136/jmedgenet-2014-102633  

  • May 6, 2015
  • 09:42 AM
  • 201 views

Video Tip of the Week: Human Phenotype Ontology, HPO

by Mary in OpenHelix

Typically, our Tips-of-the-Week cover a specific software tool or feature that we think readers would maybe like to try out. But this week’s tip is a bit different. It’s got a conceptual piece that is important, as well as referencing several software tools that work with this crucial concept to enable interoperability of many tools, […]... Read more »

Deans Andrew R., Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, & Laurel D. Cooper. (2015) Finding Our Way through Phenotypes. PLoS Biology, 13(1). DOI: http://dx.doi.org/10.1371/journal.pbio.1002033  

Kohler, S., Doelken, S., Mungall, C., Bauer, S., Firth, H., Bailleul-Forestier, I., Black, G., Brown, D., Brudno, M., Campbell, J.... (2013) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1026  

Köhler, S., Schulz, M., Krawitz, P., Bauer, S., Dölken, S., Ott, C., Mundlos, C., Horn, D., Mundlos, S., & Robinson, P. (2009) Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies. The American Journal of Human Genetics, 85(4), 457-464. DOI: 10.1016/j.ajhg.2009.09.003  

Zemojtel, T., Kohler, S., Mackenroth, L., Jager, M., Hecht, J., Krawitz, P., Graul-Neumann, L., Doelken, S., Ehmke, N., Spielmann, M.... (2014) Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Science Translational Medicine, 6(252), 252-252. DOI: 10.1126/scitranslmed.3009262  

Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M., Ray, P.... (2013) PhenoTips: Patient Phenotyping Software for Clinical and Research Use. Human Mutation, 34(8), 1057-1065. DOI: 10.1002/humu.22347  

  • April 29, 2015
  • 09:36 AM
  • 154 views

Video Tip of the Week: Proband for pedigrees with your iPad

by Mary in OpenHelix

For this week’s Tip of the Week we revisit pedigree tools. We see a lot of interest in pedigree tools from researchers and from the public, in fact. Families have been encouraged to collect their own family histories by the Surgeon General’s office in the US. We’ve been big fans of the web-based Madeline 2.0 […]... Read more »

  • April 27, 2015
  • 08:34 AM
  • 140 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
  • 166 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
  • 185 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
  • 151 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
  • 148 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
  • 200 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
  • 187 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
  • 186 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  

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