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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
246 posts

Trey
4 posts

Jennifer
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  • April 27, 2016
  • 09:39 AM
  • 66 views

Video Tip of the Week: SoyBase CMap

by Mary in OpenHelix

Over the years I’ve started to follow a lot of farmers on twitter. It might sound odd to folks who are immersed in human genomics and disease. But I actually find the plant and animal genomics communities to be pushing tech faster and further to the hands of end-users than a lot of the clinical […]... Read more »

Grant, D., Nelson, R., Cannon, S., & Shoemaker, R. (2009) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp798  

  • April 20, 2016
  • 09:36 AM
  • 129 views

Video Tip of the Week: Pathfinder, for exploring paths through data sets

by Mary in OpenHelix

I didn’t expect to do another tip on the paths through experiments or data this week. But there must be something in the water cooler lately, and all of these different tools converged on my part of the bioinformatics ecosphere. As I was perusing my tweetdeck columns, a new tool from the folks who do […]... Read more »

Christian Partl, Samuel Gratzl, Marc Streit, Anne Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg, & Alexander Lex. (2016) Pathfinder: Visual Analysis of Paths in Graphs. Computer Graphics Forum . info:other/

  • April 13, 2016
  • 09:36 AM
  • 162 views

Video Tip of the Week: Branch, a web-based tool offering decision trees for data analysis

by Mary in OpenHelix

Recently I highlighted a decision tree tool for experimental design. EDA, or Experimental Design Assistant, helps you to plan your experiment, choose the approrpiate groups and numbers you’ll need. Set some variables, etc. This week’s video also offers decision trees–but these help you to evaluate the data from your studies of interest instead. Branch is a […]... Read more »

  • April 6, 2016
  • 09:54 AM
  • 165 views

Video Tip of the Week: RGD’s OLGA tool, Object List Generator and Analyzer

by Mary in OpenHelix

One of the really persistent issues in genomics is how to either get a list of things, or handle a list of things. or the overlap among the things. I think that was one of the most popular topics we dealt with in the early days of OpenHelix, but it’s still a issue that people need to […]... Read more »

Shimoyama, M., De Pons, J., Hayman, G., Laulederkind, S., Liu, W., Nigam, R., Petri, V., Smith, J., Tutaj, M., Wang, S.... (2014) The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku1026  

  • March 30, 2016
  • 09:36 AM
  • 169 views

Video Tip of the Week: EDA, Experimental Design Assistant

by Mary in OpenHelix

Most of the bioinformatics tools we examine are things that come into play downstream of an experiment. People wish to analyze their data, look at genes that popped up (or dropped down), visualize relationships, etc. So this week’s Video Tip tool is unusual–it’s software that helps people design the upstream pieces of their experiments. Experimental […]... Read more »

  • March 23, 2016
  • 09:56 AM
  • 183 views

Video Tip of the Week: Multi-region visualization in the UCSC Genome Browser

by Mary in OpenHelix

This week’s video tip demonstrates a new feature at the UCSC Genome Browser. I think it’s kind of unusual, and conceptually took me a little while to get used to when I started testing it. So I wanted to go over the basics for you, and give you a couple of tips on things that […]... Read more »

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A.... (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Research, 44(D1). DOI: 10.1093/nar/gkv1275  

  • March 16, 2016
  • 09:42 AM
  • 207 views

Video Tip of the Week: GenomeSpace Orientation

by Mary in OpenHelix

The GenomeSpace site has been highlighted before in our “tips of the week”. We appreciated this site that pulled together a lot of different useful types of data sources and analysis strategies. On their site they describe their ethos as “Frictionless connection of bioinformatics tools”. Since that time (2012), it’s continued to grow and provide […]... Read more »

Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., Borges-Rivera, D., Pochet, N., Robinson, J., Demchak, B.... (2016) Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods, 13(3), 245-247. DOI: 10.1038/nmeth.3732  

  • March 9, 2016
  • 09:41 AM
  • 244 views

Video Tip of the Week: Introduction to Biocuration and the career path

by Mary in OpenHelix

At OpenHelix, we’ve long sung the praises of curators. Some of us have been curators and worked with curation and database development teams. All of us have relied on quality information in the databases for research and teaching. But I think there are a lot of people who don’t understand the value of quality curation, how […]... Read more »

COMMITTEE ON FUTURE CAREER OPPORTUNITIES AND EDUCATIONAL REQUIREMENTS FOR, & DIGITAL CURATION. (2015) PREPARING THE WORKFORCE FOR DIGITAL CURATION. National Academies Press. info:/10.17226/18590

Holliday, G., Bairoch, A., Bagos, P., Chatonnet, A., Craik, D., Finn, R., Henrissat, B., Landsman, D., Manning, G., Nagano, N.... (2015) Key challenges for the creation and maintenance of specialist protein resources. Proteins: Structure, Function, and Bioinformatics, 83(6), 1005-1013. DOI: 10.1002/prot.24803  

  • March 2, 2016
  • 09:38 AM
  • 201 views

Video Tip of the Week: JBrowse at Araport

by Mary in OpenHelix

The JBrowse genome browser has been around for a long time now. In fact, our first mention of it on the blog was in 2009, apparently. But we’ve talked about it a number of times since as it continued to develop. Lately, though, I’m seeing more resources that are offering JBrowse in addition to their […]... Read more »

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  

Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009) JBrowse: A next-generation genome browser. Genome Research, 19(9), 1630-1638. DOI: 10.1101/gr.094607.109  

  • February 24, 2016
  • 09:42 AM
  • 255 views

Video Tip of the Week: ContentMine, with a #Zika example

by Mary in OpenHelix

For quite a while I’ve been watching the development of ContentMine. There have been a number of different ways to text-mine the scientific literature over the years. Most of the efforts I’m familiar with aim at a specific subset of the literature. This could be species-specific mining, topic-specific (such as interaction data, or a field […]... Read more »

  • February 17, 2016
  • 09:38 AM
  • 230 views

Video Tip of the Week: Viral Resources at NCBI (including new #ZikaResearch module)

by Mary in OpenHelix

It would be hard to escape hearing and reading about the recent drama about the Zika virus. But in terms of viral genomics, that only serves to highlight how important it is to deliver quality sequence information for researchers. So in a timely coincidence, a recent lecture for the CDC on the Viral Resources at […]... Read more »

Brister, J., Ako-adjei, D., Bao, Y., & Blinkova, O. (2014) NCBI Viral Genomes Resource. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku1207  

  • February 10, 2016
  • 08:33 AM
  • 237 views

Tip of the Week: The Cancer Genome Atlas Clinical Explorer

by Mary in OpenHelix

Accessing TCGA cancer data has been approached in a variety of ways. This week’s tip of the week highlights a web-based portal for improved access to the data in different ways. The Stanford Cancer Genome Atlas Clinical Explorer is aimed at helping identify clinically relevant genes in the cancer data sets. They note that the data […]... Read more »

  • February 3, 2016
  • 09:36 AM
  • 248 views

Video Tip of the Week: SGD’s Variant Viewer

by Mary in OpenHelix

Variant viewers are very popular. As we get more and more sequence data, the challenge of looking across many samples only gets more and more important. So I always like to see how different groups are doing this. I’m still waiting for the killer app on this–the pan-genome graphs with all the paths along different […]... Read more »

Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E., Christie, K., Costanzo, M., Dwight, S., Engel, S.... (2011) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr1029  

Sheppard, T., Hitz, B., Engel, S., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M., Dalusag, K., Demeter, J., Hellerstedt, S.... (2016) The Genome Database Variant Viewer . Nucleic Acids Research, 44(D1). DOI: 10.1093/nar/gkv1250  

  • January 27, 2016
  • 09:42 AM
  • 241 views

Video Tip of the Week: Complex Portal with Super Curators

by Mary in OpenHelix

From the same team that brings us the IntAct database for protein interaction data, the Complex Portal offers insights for additional levels of protein interactions that are organized around a biological function. Although there are various resources that store individual interactions between proteins, collecting additional interactions in units of a complex are specially challenging for various […]... Read more »

Meldal, B., Forner-Martinez, O., Costanzo, M., Dana, J., Demeter, J., Dumousseau, M., Dwight, S., Gaulton, A., Licata, L., Melidoni, A.... (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku975  

  • January 20, 2016
  • 09:36 AM
  • 279 views

Video Tip of the Week: LilBUBome sequencing project

by Mary in OpenHelix

Ok, the phrase “Lil Bub is an American celebrity cat….” is not the way I start a lot of blog posts. I enjoy cats on the internet as much as anyone–but their relevance to science is not one of the reasons, usually. But the Lil Bub genome project changes that. A popular, crowd-funded, genome sequencing project […]... Read more »

  • January 13, 2016
  • 09:40 AM
  • 260 views

Video Tip of the Week: Digital Expression Explorer for RNA-seq

by Mary in OpenHelix

Coming over my digital transom in a couple of different ways recently, the Digital Expression Explorer caught my attention. I have a soft spot for expression. It’s the business end of what’s going on, not just the archives of genomic info stored up in the nucleus, you know? Heh. Anyway–I saw the poster via email […]... Read more »

Ziemann M., Kaspi A., Lazarus R., & El-Osta A. (2015) Digital Expression Explorer: A user-friendly repository of uniformly processed RNA-seq data. . ComBio2015. info:/10.13140/RG.2.1.1707.5926

  • January 6, 2016
  • 09:38 AM
  • 292 views

Video Tip of the Week: UniProt updates, now including portable BED files

by Mary in OpenHelix

UniProt is one of the core resources that provides tremendously important curated information about proteins. You will find links to UniProt in lots of other tools and databases as well, but we’ve always championed going directly there for the full look at all the wide range of information they offer. Their foundation remains solid, but […]... Read more »

The UniProt Consortium. (2014) UniProt: a hub for protein information. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku989  

  • December 16, 2015
  • 09:49 AM
  • 294 views

Video Tip of the Week: Plant Reactome at Gramene

by Mary in OpenHelix

Reactome is one of our favorite tools to explore pathways. And they cover a wide range of species, which is helpful for many researchers. But there are times when having a topic-specific tool can be even more useful for a research community. Sometimes these types of tools are disease-specific, or in the case of today’s Video Tip […]... Read more »

Tello-Ruiz, M., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J.... (2015) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research. DOI: 10.1093/nar/gkv1179  

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S.... (2015) The Reactome pathway Knowledgebase. Nucleic Acids Research. DOI: 10.1093/nar/gkv1351  

  • December 10, 2015
  • 10:13 AM
  • 327 views

What’s the Answer? (what’s up with the tardigrades?)

by Mary in OpenHelix

This week’s discussion is different. But it’s a neat look at the issues of genome assembly, contamination, over-prediction and under-prediction. If you haven’t been following the drama, it began with the paper covered in this story by Ed Yong: Inside the Bizarre Genome of the World’s Toughest Animal. This group suggested that upwards of 17% of […]... Read more »

Boothby, T., Tenlen, J., Smith, F., Wang, J., Patanella, K., Osborne Nishimura, E., Tintori, S., Li, Q., Jones, C., Yandell, M.... (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences, 201510461. DOI: 10.1073/pnas.1510461112  

Georgios Koutsovoulos, Sujai Kumar, Dominik R Laetsch, Lewis Stevens, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Aziz Aboobaker, & Mark Blaxter. (2015) The genome of the tardigrade Hypsibius dujardini. bioRxiv. DOI: 10.1101/033464  

  • December 9, 2015
  • 09:41 AM
  • 295 views

Video Tip of the Week: Send UCSC Genome Browser sequence to external tools

by Mary in OpenHelix

The folks at the UCSC Genome Browser are always adding new features, new data, and new genomes to their site. And although they use the genome-announce mailing list to get the word out, even I can miss a notice. There was news recently of a new feature associated with the graphical genome browser that I’ve […]... Read more »

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A.... (2015) The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. DOI: 10.1093/nar/gkv1275  

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