Mary

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OpenHelix
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  • August 26, 2015
  • 09:40 AM
  • 58 views

Video Tip of the Week: Human Metabolome Database, HMDB

by Mary in OpenHelix

The HMDB, or Human Metabolome DataBase, is another nice data collection and tools from the Wishart lab. Although we have mentioned it in the past, because of it’s emphasis more on small molecules it isn’t something we covered in detail. But with this new video that’s available, I thought it was a good time to […]... Read more »

Wishart, D., Jewison, T., Guo, A., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E.... (2012) HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Research, 41(D1). DOI: 10.1093/nar/gks1065  

  • August 19, 2015
  • 09:40 AM
  • 115 views

Video Tip of the Week: gene.iobio for genome and variation browsing

by Mary in OpenHelix

Twitter erupted recently with some chatter about a new tool that people seemed to really like. The iobio team from the Marth lab had launched a new gene “app” on their iobio framework. Here was some of the response: Slick! Gene.iobio tool to interactively examine #genetic variants in patient sample #genomics http://t.co/2SXGNSQhub pic.twitter.com/Hyet4j55Mc — Julie […]... Read more »

Miller, C., Qiao, Y., DiSera, T., D'Astous, B., & Marth, G. (2014) bam.iobio: a web-based, real-time, sequence alignment file inspector. Nature Methods, 11(12), 1189-1189. DOI: 10.1038/nmeth.3174  

  • August 12, 2015
  • 09:41 AM
  • 110 views

Video Tip of the Week: World Tour of Genomics Resources, part II

by Mary in OpenHelix

This week’s tip is not our usual short video. We’ll connect you to our newest tutorial suite, our World Tour of Genomics Resources, part II. Our previous tour was really popular–because as much as bench researchers know about the tools they currently use–everyone realizes there are more tools out there. And many of them don’t […]... Read more »

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

  • August 5, 2015
  • 09:38 AM
  • 109 views

Video Tip of the Week: Araport, Arabidopsis Portal

by Mary in OpenHelix

The recent Plant Biology 2015 conference tweets were full of delightful morsels (#plantbiology15). Some of them edible. I am very psyched to learn of the Legume Federation. Legumes are *way* at the top of my list of favorite organisms. I think it was their tweet of the Araport data that led to this week’s video tip […]... Read more »

Hanlon, M., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E.... (2015) Araport: an application platform for data discovery. Concurrency and Computation: Practice and Experience. DOI: 10.1002/cpe.3542  

Krishnakumar, V., Hanlon, M., Contrino, S., Ferlanti, E., Karamycheva, S., Kim, M., Rosen, B., Cheng, C., Moreira, W., Mock, S.... (2014) Araport: the Arabidopsis Information Portal. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku1200  

  • July 29, 2015
  • 09:39 AM
  • 146 views

Video Tip of the Week: PathWhiz for Pathways, Part II

by Mary in OpenHelix

This week’s tip is a follow-up to the PathWhiz one featured last week. After I had finished writing that one, the second video in the series became available. It has a lot more detail on how to work with the tool. I’m not going to go into the introduction here again, you can flip back […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • July 22, 2015
  • 09:36 AM
  • 112 views

Video Tip of the Week: PathWhiz for graphical appeal and computational readability

by Mary in OpenHelix

“Pathway diagrams are the road maps of biology.” This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announced. The NAR database issue in January and the mid-year web server issue are perfectly timed items that I can content […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • July 15, 2015
  • 09:39 AM
  • 150 views

Video Tip of the Week: Introduction to the UCSC Genome Browser

by Mary in OpenHelix

This week’s tip is quite multi-media. There’s a video, as required. But there’s a traditional published paper format, too. And there’s also the free training slides and exercises from us, sponsored by the folks who create the UCSC Genome Browser. So if you prefer audio, graphics, or text–we’ve got it all in this week’s tip. […]... Read more »

Mangan ME, Williams JM, Kuhn RM, & Lathe WC. (2014) The UCSC Genome Browser: What Every Molecular Biologist Should Know. Current Protocols in Molecular Biology., 107(19.9), 199-199. DOI: 10.1002/0471142727.mb1909s107  

  • July 8, 2015
  • 09:45 AM
  • 162 views

Video Tip of the Week: PhenomeCentral

by Mary in OpenHelix

Silos. This is a big problem for us with human genome data from individuals. We’re getting sequences, but they are locked up in various ways. David Haussler’s talk at the recent Global Alliance for Genomics and Health meeting (GA4GH) emphasized this barrier, and also talked about ways they are looking to work around the legal, […]... Read more »

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  

  • July 1, 2015
  • 09:39 AM
  • 155 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
  • 189 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
  • 128 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
  • 248 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
  • 202 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
  • 247 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
  • 231 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
  • 258 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
  • 223 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
  • 175 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
  • 311 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
  • 222 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 »

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