Mary

159 posts · 75,065 views

OpenHelix
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  • October 29, 2014
  • 09:46 AM
  • 43 views

Video Tip of the Week: PaleoBioDB, for your paleobiology searches

by Mary in OpenHelix

Yeah, I know, it’s not genomics–but it’s the history of life on this planet–right?  The Paleobiology Database has been keeping records of this ancient biology for a while now, and they have some really nice tools to explore the fossil records and resources that have become available. It’s also interesting to me to see the […]... Read more »

Varela Sara, González-Hernández Javier, Sgarbi Luciano, Marshall Charles, Uhen Mark, Peters Shanan, & McClennen Michael. (2014) paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. Ecography. DOI: 10.1111/ecog.01154  

  • October 22, 2014
  • 09:46 AM
  • 75 views

Video Tip of the Week: SeqMonk

by Mary in OpenHelix

Always on the lookout for effective visualization tools, I recently came across a series of videos about the SeqMonk software. It’s not software that I had used before, so I wanted to look at the videos, and then try it out. It downloaded quickly, offered me an extensive list of genomes to load up, and […]... Read more »

  • October 15, 2014
  • 09:46 AM
  • 89 views

Video Tip of the Week: MedGen, GTR, and ClinVar

by Mary in OpenHelix

The terrific folks at NCBI have been increasing their outreach with a series of webinars recently. I talked about one of them not too long ago, and I mentioned that when I found the whole webinar I’d highlight that. This recording is now available, and if you are interested in using these medical genetics resources, […]... Read more »

Acland A., R. Agarwala, T. Barrett, J. Beck, D. A. Benson, C. Bollin, E. Bolton, S. H. Bryant, K. Canese, D. M. Church.... (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1146  

  • October 8, 2014
  • 06:49 AM
  • 97 views

Video Tip of the Week: UCSC #Ebola Genome Portal

by Mary in OpenHelix

Although I had other tips in my queue already, over the last week I’ve seen a lot of talk about the new Ebola virus portal from the UCSC Genome Browser team. And it struck me that researchers who have worked primarily on viral sequences may not be as familiar with the functions of the UCSC […]... Read more »

Karolchik D., G. P. Barber, J. Casper, H. Clawson, M. S. Cline, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler.... (2013) The UCSC Genome Browser database: 2014 update. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1168  

  • October 6, 2014
  • 11:18 AM
  • 85 views

Bioinformatics tools extracted from a typical mammalian genome project [supplement]

by Mary in OpenHelix

This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to keep in the post, but I wanted it to be web-searchable. A copy also resides at FigShare: http://dx.doi.org/10.6084/m9.figshare.1194867 Software tool/object/item/resource access […]... 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  

  • October 6, 2014
  • 11:12 AM
  • 85 views

Bioinformatics tools extracted from a typical mammalian genome project

by Mary in OpenHelix

In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the larger issues this raises in the field. It’s long, and it’s something of a hybrid between a blog post and a paper format, just to give it some structure for my […]... 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  

  • October 1, 2014
  • 09:46 AM
  • 118 views

Video Tip of the Week: MEGA, Molecular Evolutionary Genetics Analysis

by Mary in OpenHelix

This week’s tip of the week highlights the MEGA tools–MEGA is a collection of tools that perform Molecular Evolutionary Genetics Analysis. MEGA tools are not new–they’ve been developed and supported over many years. In fact, on their landing page you can see the first reference to MEGA was in 1994. How much computing were you […]... Read more »

  • September 25, 2014
  • 09:46 AM
  • 165 views

What’s the Answer? (domain and lollipop mutation diagrams)

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 »

Gao J., U. Dogrusoz, G. Dresdner, B. Gross, S. O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, & E. Cerami. (2013) Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Science Signaling, 6(269). DOI: http://dx.doi.org/10.1126/scisignal.2004088  

  • September 24, 2014
  • 09:46 AM
  • 101 views

Video Tip of the Week: StratomeX for genomic stratification of diseases

by Mary in OpenHelix

The Calyedo team and the tools they develop have been on my short list of favorites for a long time. I’ve been talking about their clever visualizations for years now. My first post on their work was in 2010, with the tip I did on their Calyedo tool that combined gene expression and pathway visualization. […]... Read more »

Streit Marc, Samuel Gratzl, Christian Partl, Dieter Schmalstieg, Hanspeter Pfister, Peter J Park, & Nils Gehlenborg. (2014) Guided visual exploration of genomic stratifications in cancer. Nature Methods, 11(9), 884-885. DOI: http://dx.doi.org/10.1038/nmeth.3088  

  • September 17, 2014
  • 09:46 AM
  • 124 views

Video Tip of the Week: GOLD, Genomes OnLine Database

by Mary in OpenHelix

Yes, I know some people suffer from YAGS-malaise (Yet Another Genome Syndrome), but I don’t. I continue to be psyched for every genome I hear about. I even liked the salmon lice one. And Yaks. The crowd-funded Puerto Rican parrot project was so very neat. These genomes may not matter much for your everyday life, […]... Read more »

Liolios Konstantinos, Lynette Hirschman, Ioanna Pagani, Bahador Nosrat, Peter Sterk, Owen White, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris Taylor, & Nikos C. Kyrpides. (2012) The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Standards in Genomic Sciences, 6(3), 444-453. DOI: http://dx.doi.org/10.4056/sigs.2675953  

Field Dawn, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, & Michael Ashburner. (2008) The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26(5), 541-547. DOI: http://dx.doi.org/10.1038/nbt1360  

  • September 11, 2014
  • 09:37 AM
  • 61 views

What’s The Answer? (gene essentiality)

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 »

  • September 10, 2014
  • 09:36 AM
  • 142 views

Video Tip of the Week: #Docker, shipping containers for software and data

by Mary in OpenHelix

Breaking into the zeitgeist recently, Docker popped into my sphere from several disparate sources. Seems to me that this is a potential problem-solver for some of the reproducibility and sharing dramas that we have been wrestling with in genomics. Sharing of data sets and versions of analysis software is being tackled in a number of […]... Read more »

  • September 3, 2014
  • 09:46 AM
  • 146 views

Video Tip of the Week: NIH 3D Print Exchange

by Mary in OpenHelix

The other day I was joking about how I was 3D-printing a baby sweater–the old way, with yarn and knitting needles. And I also mentioned that I assumed my niece-in-law was 3D-printing the baby separately. I’ve been musing (and reading) about 3D printing a lot lately–sometimes the plastic model part, sometimes the bioprinting of tissues […]... Read more »

Murphy Sean V. (2014) 3D bioprinting of tissues and organs. Nature Biotechnology, 32(8), 773-785. DOI: http://dx.doi.org/10.1038/nbt.2958  

  • August 27, 2014
  • 09:38 AM
  • 128 views

Video Tip of the Week: Phenoscape, captures phenotype data across taxa

by Mary in OpenHelix

Development of the skeleton is a good example of a process that is highly regulated, requires a lot of precision, is conserved and important relationships across species, and is fairly easy to detect when it’s gone awry. I mean–it’s hard to know at a glance if all the neurons in an organism got to the […]... Read more »

Mabee By Paula, Balhoff James P, Dahdul Wasila M, Lapp Hilmar, Midford Peter E, Vision Todd J, & Westerfield Monte. (2012) 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift fur angewandte Ichthyologie . PMID: 22736877  

Balhoff James P., Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield, & Todd J. Vision. (2010) Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE, 5(5). DOI: http://dx.doi.org/10.1371/journal.pone.0010500  

  • August 20, 2014
  • 09:38 AM
  • 161 views

Video Tip of the Week: Immune Epitope DB (IEDB)

by Mary in OpenHelix

This week’s tip was inspired by the recent NHGRI workshop of the future directions for funding and resourcing of genomics-related projects. Titled “Future Opportunities for Genome Sequencing and Beyond: A Planning Workshop for the National Human Genome Research Institute” brought together a lot of influential folks on this topic, and had them noodle on the […]... Read more »

Vita R., J. A. Greenbaum, H. Emami, I. Hoof, N. Salimi, R. Damle, A. Sette, & B. Peters. (2010) The Immune Epitope Database 2.0. Nucleic Acids Research, 38(Database). DOI: http://dx.doi.org/10.1093/nar/gkp1004  

Kim Y., Z. Zhu, D. Tamang, P. Wang, J. Greenbaum, C. Lundegaard, A. Sette, O. Lund, P. E. Bourne, & M. Nielsen. (2012) Immune epitope database analysis resource. Nucleic Acids Research, 40(W1). DOI: http://dx.doi.org/10.1093/nar/gks438  

Bhattacharya Sanchita, Linda Gomes, Patrick Dunn, Henry Schaefer, Joan Pontius, Patty Berger, Vince Desborough, Tom Smith, John Campbell, & Elizabeth Thomson. (2014) ImmPort: disseminating data to the public for the future of immunology. Immunologic Research, 58(2-3), 234-239. DOI: http://dx.doi.org/10.1007/s12026-014-8516-1  

  • August 14, 2014
  • 12:20 PM
  • 171 views

Video Tip of the Week: EpiViz Genome Browsing (and more)

by Mary in OpenHelix

This is the browser I’ve been waiting for. Stop what you are doing right now and look at EpiViz. I’ll wait.

I spend a lot of time looking at visualizations of various types of -omics data, from a number of different sources. I’ve never believed in the “one browser to rule them all” sort of thing–I think it’s important for groups to focus on special areas of data collection, curation, and visualizion. Although some parts can be reused and shared, of co........ Read more »

Chelaru Florin, Smith Llewellyn, Goldstein Naomi, & Bravo Héctor Corrada. (2014) Epiviz: interactive visual analytics for functional genomics data. Nature methods. PMID: 25086505  

  • August 6, 2014
  • 09:36 AM
  • 169 views

Video Tip of the Week: Biodalliance browser with HiSeq X-Ten data

by Mary in OpenHelix

Drama surrounding the $1000 genome erupts every so often, and earlier this year when the HiSeq X Ten setup was unveiled there was a lot of chatter–and questions: Is the $1,000 genome for real? And some push-back on the cost analysis: That “$1000 genome” is going to cost you $72M. A piece that offers nice […]... Read more »

Dunham Ian, Shelley F. Aldred, Patrick J. Collins, Carrie A. Davis, Francis Doyle, Charles B. Epstein, Seth Frietze, Jennifer Harrow, Rajinder Kaul, & Jainab Khatun. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. DOI: http://dx.doi.org/10.1038/nature11247  

  • July 31, 2014
  • 09:22 AM
  • 176 views

What’s the Answer? (electronic lab notebooks)

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 »

Voegele C., N. Robinot, J. McKay, P. Damiecki, & L. Alteyrac. (2013) A universal open-source Electronic Laboratory Notebook. Bioinformatics, 29(13), 1710-1712. DOI: http://dx.doi.org/10.1093/bioinformatics/btt253  

  • July 30, 2014
  • 09:41 AM
  • 170 views

Video Tip of the Week: PhenDisco, “phenotype discoverer” for dbGap data

by Mary in OpenHelix

The dbGaP, database of Genotypes and Phenotypes, repository at NCBI collects information from research projects that link genotype and phenotype information and human variation, across many different types of studies, providing leads on variation that may be important to understand clinical issues. Some of the data is publicly available de-identified patient information, and some of the […]... Read more »

Doan Son, Lin Ko-Wei, Conway Mike, Ohno-Machado Lucila, Hsieh Alex, Feupe Stephanie Feudjio, Garland Asher, Ross Mindy K, Jiang Xiaoqian, & Farzaneh Seena. (2013) PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal of the American Medical Informatics Association : JAMIA. PMID: 23989082  

Tryka K. A., A. Sturcke, Y. Jin, Z. Y. Wang, L. Ziyabari, M. Lee, N. Popova, N. Sharopova, M. Kimura, & M. Feolo. (2013) NCBI's Database of Genotypes and Phenotypes: dbGaP. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1211  

  • July 23, 2014
  • 09:38 AM
  • 161 views

Video Tip of the Week: Nowomics, set up alert feeds for new data

by Mary in OpenHelix

Yeah, I know you know. There’s a lot of genomics and proteomics data coming out every day–some of it in the traditional publication route, but some of it isn’t–and it’s only getting harder and harder to wrangle the useful information to access the signal from the noise.  I can remember when merely looking through the […]... Read more »

Acland A., T. Barrett, J. Beck, D. A. Benson, C. Bollin, E. Bolton, S. H. Bryant, K. Canese, D. M. Church, & K. Clark. (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1146  

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