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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
145 posts

Trey
4 posts

Jennifer
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  • August 20, 2014
  • 09:38 AM
  • 53 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
  • 72 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
  • 89 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
  • 98 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
  • 88 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
  • 82 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  

  • July 22, 2014
  • 09:08 AM
  • 93 views

A History of Bioinformatics (told from the Year 2039)

by Mary in OpenHelix

A week or so back I was watching the chatter around the #ISMB / #BOSC2014 meeting, and saw a number of amusing and intriguing comments about Titus Brown’s keynote talk. [embedded tweets] You can see a lot of chatter about it in the Storify. I was delighted to soon see this follow up...... Read more »

  • July 16, 2014
  • 09:37 AM
  • 100 views

Video Tip of the Week: VectorBase, for invertebrate vectors of human pathogens

by Mary in OpenHelix

I wish I had been clever enough to coordinate this week’s Video Tip of the Week with “Mosquito Week” a couple of months back. There was a bunch of chatter at that time about this infographic that was released by Bill Gates, which illustrated the contribution of various human-killing species. The mosquito was deemed: The […]... Read more »

Megy K., D. Lawson, D. Campbell, E. Dialynas, D. S. T. Hughes, G. Koscielny, C. Louis, R. M. MacCallum, S. N. Redmond, & A. Sheehan. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research, 40(D1). DOI: http://dx.doi.org/10.1093/nar/gkr1089  

  • July 9, 2014
  • 09:37 AM
  • 106 views

Video Tip of the Week: Google Genomics, API and GAbrowse

by Mary in OpenHelix

This week’s video tip comes to us from Google–it’s about their participation in the “Global Alliance for Genomics and Health” coalition. Global Alliance is aimed at developing genomic data standards for interoperability, and they’ve been working on creating the framework (some background links below in the references will provide further details). It has over 170 […]... Read more »

  • July 3, 2014
  • 09:59 AM
  • 139 views

What’s the Answer? (mutation nomenclature)

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 »

  • July 2, 2014
  • 09:36 AM
  • 116 views

Video Tip of the Week: NCBI Variation Viewer

by Mary in OpenHelix

The folks at NCBI recently hosted a webinar that covered a number of resources: GTR, ClinVar, and MedGen. It was a nice introduction to these resources using a case study of exploring information about a 9-year-old child who needed to get clearance for participation in sports. So they follow the course of some details about […]... Read more »

Landrum M. J., G. R. Riley, W. Jang, W. S. Rubinstein, D. M. Church, & D. R. Maglott. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(D1). DOI: http://dx.doi.org/10.1093/nar/gkt1113  

  • June 25, 2014
  • 09:37 AM
  • 185 views

Video Tip of the Week: Leukemia outcome predictions challenge

by Mary in OpenHelix

Although I had other tips in the pipeline, I’m bumping this one up because it is time sensitive. It’s about a competition (or challenge, as they describe it) to use data from cases of leukemia to model make predictions about the outcomes, which could help drive treatment decisions someday. It is called the Acute Myeloid […]... Read more »

Boutros Paul C, Kyle Ellrott, Thea C Norman, Kristen K Dang, Yin Hu, Michael R Kellen, Christine Suver, J Christopher Bare, Lincoln D Stein, & Paul T Spellman. (2014) Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics, 46(4), 318-319. DOI: http://dx.doi.org/10.1038/ng.2932  

  • June 19, 2014
  • 09:37 AM
  • 125 views

What’s The Answer? (explosion of careers)

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 »

  • June 18, 2014
  • 09:38 AM
  • 140 views

Video Tip of the Week: e-PathGen, Using Genomics to Support Public Health

by Mary in OpenHelix

Recently I saw the Director of Public Health Genomics for the CDC tweet about a resource that was new to me, ePathGen, Pathogen Genomics for Epidemiology. This is an area that I’m glad to see getting attention. My undergrad degree was in microbiology, and certainly the most memorable class I had in college was about pathogenic […]... Read more »

  • June 12, 2014
  • 09:43 AM
  • 81 views

What’s the Answer? (aligning isoforms)

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 »

  • June 11, 2014
  • 09:36 AM
  • 133 views

Video Tip of the Week: InterMine for complex queries

by Mary in OpenHelix

We’ve been fans of InterMine for a long time. We did a tip-of-the-week in a while ago that highlighted ways that this software can be used to mine from big data projects of many types. The generic framework of InterMine can be customized for use at different projects–today I’ll include videos from the FlyMine installation […]... Read more »

Smith Richard N, Aleksic Jelena, Butano Daniela, Carr Adrian, Contrino Sergio, Hu Fengyuan, Lyne Mike, Lyne Rachel, Kalderimis Alex, & Rutherford Kim. (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics (Oxford, England). DOI: 10.1093/bioinformatics/bts577  

Lyne Rachel, Smith Richard, Rutherford Kim, Wakeling Matthew, Varley Andrew, Guillier Francois, Janssens Hilde, Ji Wenyan, Mclaren Peter, & North Philip. (2012) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome biology. PMID: 17615057  

Balakrishnan Rama, Park Julie, Karra Kalpana, Hitz Benjamin C, Binkley Gail, Hong Eurie L, Sullivan Julie, Micklem Gos, & Cherry J Michael. (2012) YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database : the journal of biological databases and curation. PMID: 22434830  

Sullivan Julie, Karra Kalpana, Moxon Sierra A T, Vallejos Andrew, Motenko Howie, Wong J D, Aleksic Jelena, Balakrishnan Rama, Binkley Gail, & Harris Todd. (2013) InterMOD: integrated data and tools for the unification of model organism research. Scientific reports, 3( 1802 1802). PMID: 23652793  

  • June 4, 2014
  • 06:25 AM
  • 158 views

Video Tip of the Week: LineUp, data ranking visualization tool

by Trey in OpenHelix

  Caleydo, from the Institute of Computer Graphics and Vision, a suite of genomics and biomolecular visualization tools. As the project developers state, it’s strength is “the visualization of interdependencies between multiple datasets.” The tip of the week this week is a video introducing one of their newest tools: LineUp. LineUp is an open source […]... Read more »

Gratzl S, Lex A, Gehlenborg N, Pfister H, & Streit M. (2013) LineUp: visual analysis of multi-attribute rankings. IEEE transactions on visualization and computer graphics, 19(12), 2277-86. PMID: 24051794  

  • May 28, 2014
  • 09:42 AM
  • 132 views

Video Tip of the Week: New UCSC “stacked” wiggle track view

by Mary in OpenHelix

This week’s video tip shows you a new way to look at the multiWig track data at the UCSC Genome Browser. A new option has recently been released (see 06 May 2014), a “stacked” view, and it’s a handy way to look at the data with a new strategy. But I’ll admit it took me […]... Read more »

Kent W J, Zweig A S, Barber G, Hinrichs A S, & Karolchik D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (Oxford, England). PMID: 20639541  

Karolchik Donna, Barber Galt P, Casper Jonathan, Clawson Hiram, Cline Melissa S, Diekhans Mark, Dreszer Timothy R, Fujita Pauline A, Guruvadoo Luvina, & Haeussler Maximilian. (2013) The UCSC Genome Browser database: 2014 update. Nucleic acids research. PMID: 24270787  

The ENCODE Project Consortium, Bernstein Bradley E, Birney Ewan, Dunham Ian, Green Eric D, Gunter Chris, & Snyder Michael. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature. PMID: 22955616  

  • May 21, 2014
  • 09:33 AM
  • 153 views

Video Tip of the Week: PhenX, standardizing phenotype measurements

by Mary in OpenHelix

This week’s tip is actually sort of a mega-tip. It’s not just one video–it’s a series of videos that the GeneticAlliance has provided (and there are more to come) with the theme: “Managing the Mass of Measures: Real People’s Real Data Made Useful”. It is part of their Standards and Tools webinar series that is […]... Read more »

Hamilton C. M., Strader L. C., Pratt J. G., Maiese D., Hendershot T., Kwok R. K., Hammond J. A., Huggins W., Jackman D., & Pan H. (2011) The PhenX Toolkit: Get the Most From Your Measures. American Journal of Epidemiology, 174(3), 253-260. DOI: 10.1093/aje/kwr193  

  • May 14, 2014
  • 09:42 AM
  • 143 views

Video Tip of the Week: PheGenI, Phenotype-Genotype Integrator

by Mary in OpenHelix

The hunt for variations in genes and genomes has been both fruitful and frustrating. We can see genome variations in a variety of ways, but we can’t always connect them with a phenotype easily. And vice versa, of course. Another problem is that the kinds of data that we want to mine for further analysis […]... Read more »

Ramos Erin M, Hoffman Douglas, Junkins Heather A, Maglott Donna, Phan Lon, Sherry Stephen T, Feolo Mike, & Hindorff Lucia A. (2013) Phenotype–Genotype Integrator (PheGenI): synthesizing genome-wide association study (GWAS) data with existing genomic resources. European Journal of Human Genetics, 22(1), 144-147. DOI: 10.1038/ejhg.2013.96  

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