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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
165 posts

Trey
4 posts

Jennifer
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  • November 26, 2014
  • 07:12 AM
  • 46 views

Thanksgiving week, light posting. One holiday genome (cranberries).

by Mary in OpenHelix

There’s nobody reading the blog this week each year, everyone is traveling or napping, at least in the US. So I’ll just bring a holiday genome I came across recently. Cranberries. This fruit is one of very few native North American fruits that are widely cultivated. I went looking to see if a genome paper […]... Read more »

  • November 25, 2014
  • 01:18 PM
  • 66 views

Oy. I worry about this with cell line studies a lot. Mis-IDed contaminated.

by Mary in OpenHelix

Via NCBI Announce mailing list: NCBI BioSample includes curated list of over 400 known misidentified and contaminated cell lines The NCBI BioSample database now includes a curated list of over 400 known misidentified and contaminated cell lines. Scientists should check this list before they start working with a new cell line to see if that cell line […]... Read more »

American Type Culture Collection Standards Development Organization Workgroup ASN-0002. (2010) Cell line misidentification: the beginning of the end. Nature Reviews Cancer, 10(6), 441-448. DOI: http://dx.doi.org/10.1038/nrc2852  

  • November 19, 2014
  • 09:50 AM
  • 81 views

Video Tip of the Week: GeneFriends

by Mary in OpenHelix

It was just a little tweet, with hardly any information about the function or purpose of the resource mentioned. But the cute name drove a lot of people to take a look at GeneFriends from our blog recently, so I figured it was worth highlighting this tool as our Video Tip of the Week. So […]... Read more »

  • November 12, 2014
  • 08:08 AM
  • 98 views

Video Tip of the Week: UpSet about genomics Venn Diagrams?

by Mary in OpenHelix

Who can forget the Banana Venn? It was one of the most talked-about visualizations in genomics that I’m aware of. A new concept in data visualization: the Venn/banana diagram. MT @phylogenomics http://t.co/xjitNDNl — Iddo Friedberg (@iddux) July 19, 2012 Banana? RT @phylogenomics: Perhaps the best genomics Venn diagram ever #Bananas #NotSureWhatItMeansButDontCare http://t.co/xMV25GBG — Brian Kent […]... Read more »

D’Hont Angélique, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, & Corinne Da Silva. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213-217. DOI: http://dx.doi.org/10.1038/nature11241  

Lex Alexander , Gehlenborg Nils , Strobelt Hendrik , Vuillemot Romain Vuillemot, & Pfister Hanspeter . (2014) UpSet: Visualization of Intersecting Sets. IEEE Transactions on Visualization and Computer Graphics (InfoVis '14). info:other/TBD

Gibbs Richard A., Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch, & Geoffrey Okwuonu. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982), 493-521. DOI: http://dx.doi.org/10.1038/nature02426  

  • November 10, 2014
  • 09:48 AM
  • 74 views

Genome Editing with CRISPR-Cas9, nifty animation

by Mary in OpenHelix

I saw this come across my twitter feed the other day, and as a nice Friday afternoon diversion I posted it to Google+. I was surprised how popular it was. So I thought–hey, I have a blog too. Let’s put it there…. So grab some coffee and watch, a nice gentle way to get your […]... Read more »

Platt Randall J., Sidi Chen, Yang Zhou, Michael J. Yim, Lukasz Swiech, Hannah R. Kempton, James E. Dahlman, Oren Parnas, Thomas M. Eisenhaure, Marko Jovanovic.... (2014) CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Cell, 159(2), 440-455. DOI: http://dx.doi.org/10.1016/j.cell.2014.09.014  

  • November 5, 2014
  • 09:47 AM
  • 80 views

Video Tip of the Week: Genome Browser in a Box

by Mary in OpenHelix

We’ve been doing UCSC Genome Browser training workshops for a decade now. We’ve seen all sorts of situations–from places that had terrific bioinformatics and IT support, to places where the attendees had no idea if anyone provided support at their institution. Ironically, sometimes the places with little support were big-name research places where all the […]... Read more »

Haeussler M., B. J. Raney, A. S. Hinrichs, H. Clawson, A. S. Zweig, D. Karolchik, J. Casper, M. L. Speir, D. Haussler, & W. J. Kent. (2014) Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. DOI: http://dx.doi.org/10.1093/bioinformatics/btu712  

  • October 29, 2014
  • 09:46 AM
  • 95 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
  • 106 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
  • 118 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
  • 124 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
  • 113 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
  • 119 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
  • 153 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
  • 189 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
  • 134 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
  • 159 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
  • 94 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
  • 168 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
  • 169 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
  • 154 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  

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