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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
253 posts

Trey
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Jennifer
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  • June 15, 2016
  • 09:37 AM
  • 392 views

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

by Mary in OpenHelix

The team at UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option.  When it was first launched, I did a tip on how to use that, with some of the things that I noticed […]... 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  

  • June 8, 2016
  • 09:37 AM
  • 356 views

Video Tip of the Week: MyGene2, connecting families with rare conditions with each other

by Mary in OpenHelix

Last week’s tip encouraged people to think about how their DNA may be used by various stakeholders. This could be researchers, physicians, pharmaceutical companies, and so on. But one thing it didn’t really cover–now that I think of it–was connecting with other families who may share variations that impact the health of someone in their […]... Read more »

  • June 1, 2016
  • 09:38 AM
  • 386 views

Video Tip of the Week: Your DNA, Your Say. GA4GH wants to hear from you. And you.

by Mary in OpenHelix

The Global Alliance for Genomics and Health (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the […]... Read more »

  • May 25, 2016
  • 08:31 AM
  • 367 views

Video Tip of the Week: ProSplign in NCBI’s Genome Workbench

by Mary in OpenHelix

There are many tools at NCBI, with a huge range of functions. Literature, sequence data, variations, protein structure, chemicals and bioassays, and more. It’s hard to keep track of what’s available. Their video tutorials are helping me to be aware of new tools, and new features within existing tools. For this week’s Tip of the […]... Read more »

  • May 18, 2016
  • 09:36 AM
  • 495 views

Video Tip of the Week: JGI user meeting videos, and MetaSUB

by Mary in OpenHelix

This week’s Video Tip of the Week is actually a whole bunch of videos. Although I’ll highlight one here as our tip, there are many great talks from the recent JGI Genomics of Energy & Environment meeting. Although typically we focus on specific software tools for our tips, I think this is a nice case […]... Read more »

Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J., Reeves, D., Gandara, J., Chhangawala, S.... (2015) Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems, 1(1), 72-87. DOI: 10.1016/j.cels.2015.01.001  

Alexa B.R. McIntyre, Lindsay Rizzardi, Angela M Yu, Gail L. Rosen, Noah Alexander, Douglas J. Botkin, Kristen K. John, Sarah L. Castro-Wallace, Aaron S. Burton, Andrew Feinberg.... (2015) Nanopore Sequencing in Microgravity. bioRxiv. DOI: 10.1101/032342  

  • May 11, 2016
  • 08:05 AM
  • 338 views

Video Tip of the Week: New UCSC Genome Browser Gateway look

by Mary in OpenHelix

For years now we’ve been doing training and outreach on the UCSC Genome Browser. And there’s been a lot of change over the years–so much more data, so many new tools, new species. All that ENCODE information and a portal for that. But the look of the main site was largely the same. Here’s a […]... 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  

  • May 4, 2016
  • 09:38 AM
  • 508 views

Video Tip of the Week: expVIP, an Expression, Visualization, and Integration Platform

by Mary in OpenHelix

As I mentioned last week, I am watching a lot of farmers on twitter talk about this year’s North American growing season. To get a taste of that yourself, have a look at #Plant16 + wheat as a search. This is where the rubber of tractor tires and plant genomics hits the…well…rows. And just coincidentally […]... Read more »

Philippa Borrill, Ricardo Ramirez-Gonzalez, & Cristobal Uauy. (2016) expVIP: a customisable RNA-seq data analysis and visualisation platform. Plant Physiology, 2172-2186. info:/10.​1104/​pp.​15.​01667

  • April 27, 2016
  • 09:39 AM
  • 351 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
  • 466 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
  • 442 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
  • 426 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
  • 488 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
  • 450 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
  • 465 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
  • 674 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
  • 412 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
  • 622 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
  • 456 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
  • 460 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
  • 471 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  

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