Mary

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OpenHelix
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  • February 3, 2016
  • 09:36 AM
  • 69 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
  • 99 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
  • 112 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
  • 124 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
  • 153 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
  • 168 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
  • 211 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
  • 183 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  

  • December 3, 2015
  • 09:21 AM
  • 192 views

What’s the Answer? (Dare we edit the human race?) #GeneEditSummit

by Mary in OpenHelix

This week’s question is a biggie. And there’s no answer yet. But that is the topic of the National Academies big event this week, International Summit on Human Gene Editing. I have been glued to this for the whole time and didn’t spend much time looking for questions this week. And I’ll be watching the final […]... Read more »

  • December 2, 2015
  • 09:45 AM
  • 229 views

Video Tip of the Week: KBase, DOE’s Systems Biology Knowledgebase

by Mary in OpenHelix

I’ve been following the development of KBase for a long time. A couple of times I started draft blog posts to highlight them. But it always seemed like they were just about ready to launch some new features–so I figured I’d wait–or they had a beta interface in testing and about to change a lot […]... Read more »

Wilke, A., Bischof, J., Harrison, T., Brettin, T., D'Souza, M., Gerlach, W., Matthews, H., Paczian, T., Wilkening, J., Glass, E.... (2015) A RESTful API for Accessing Microbial Community Data for MG-RAST. PLoS Computational Biology, 11(1). DOI: 10.1371/journal.pcbi.1004008  

  • November 25, 2015
  • 09:50 AM
  • 221 views

Video Tip of the Week: iDigBio for access to historical specimens and more

by Mary in OpenHelix

Usually for Thanksgiving week posting is light. In the past, we’ve all done turkey breeding and genomics, cranberry genome, and some people have included apples, potatoes, and more. But another key aspect of the holiday is to remember the past and thank those who came before. And as I was watching this video that crossed my […]... Read more »

Nelson, G., Sweeney, P., Wallace, L., Rabeler, R., Allard, D., Brown, H., Carter, J., Denslow, M., Ellwood, E., Germain-Aubrey, C.... (2015) Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi. Applications in Plant Sciences, 3(9), 1500065. DOI: 10.3732/apps.1500065  

Jolley-Rogers, G., Varghese, T., Harvey, P., dos Remedios, N., & Miller, J. (2014) PhyloJIVE: Integrating biodiversity data with the Tree of Life. Bioinformatics, 30(9), 1308-1309. DOI: 10.1093/bioinformatics/btu024  

  • November 18, 2015
  • 12:46 PM
  • 242 views

Video Tip of the Week: Explore Gene Pages at NCBI with Variation and Expression Information

by Mary in OpenHelix

NCBI has produced some of the most in-depth and reliable bioinformatic tools, in large part because they’ve been building them since the earliest days of the genomics era. I once noted that I remember the oldest web interface, because it was one of the first places that I went for computational tools back in the day. […]... Read more »

  • November 11, 2015
  • 09:39 AM
  • 244 views

Video Tip of the Week: UCSC Table Browser and Custom Tracks

by Mary in OpenHelix

This week’s video tip is longer than usual. But if you want to dig deeper into all the data that you know is coming in to the UCSC Genome Browser, you want to use the Table Browser. If you’ve only used the genome browser interface, you are missing a lot of opportunity to mine for […]... Read more »

Rosenbloom, K., Armstrong, J., Barber, G., Casper, J., Clawson, H., Diekhans, M., Dreszer, T., Fujita, P., Guruvadoo, L., Haeussler, M.... (2014) The UCSC Genome Browser database: 2015 update. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku1177  

Mangan ME, Williams JM, Kuhn RM, & Lathe WC. (2014) The UCSC Genome Browser: What Every Molecular Biologist Should Know. Current Protocols in Molecular Biology., 107(19.9), 199-199. DOI: 10.1002/0471142727.mb1909s107  

  • November 4, 2015
  • 09:40 AM
  • 220 views

Video Tip of the Week: RNACentral, wrangling non-coding RNA for simplifying access

by Mary in OpenHelix

Non-coding RNA data can be tricky to locate in public data sources. Sometimes it is handled with other gene sets, other times it’s not. Some ncRNA may be found in databases of one type or one species, but it’s not always clear what the best route to find them would be. The folks from RNACentral […]... Read more »

  • October 28, 2015
  • 09:39 AM
  • 251 views

Video Tip of the Week: New Reactome Pathway Portal 3.0

by Mary in OpenHelix

The Reactome pathway browser has long been a favorite of ours. We’ve watched it evolve over the years, and continue to appreciate the organization and features that it provides for exploring pathways and interactions across a range of species. From the mailing list recently, I learned about a new version of the Reactome Pathway Portal, […]... Read more »

Croft, D., Mundo, A., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M.... (2013) The Reactome pathway knowledgebase. Nucleic Acids Research, 42(D1). DOI: 10.1093/nar/gkt1102  

  • October 22, 2015
  • 09:36 AM
  • 266 views

What’s The Answer? (what frustrates you?)

by Mary in OpenHelix

Ok, this week’s attempt to get at answers to big (and small) questions is not from one of the usual places that I do my question-mining. This came from Twitter. It started out as a request for some survey data among the bioinformatics/genomics twitterati. And it turned into a fascinating, raw, thoughtful, irreverant, and compelling […]... Read more »

Loman, Nicholas, & Connor, Thomas. (2015) Bioinformatics infrastructure and training survey. figshare. info:/

  • October 21, 2015
  • 09:38 AM
  • 233 views

Video Tip of the Week: PanelApp, from the 100000 Genomes Project

by Mary in OpenHelix

Last week I talked about the 100,000 Genomes Project in the UK. That video tip was an introduction and overview of the project. This week, though, we’ll highlight one software piece that is in place now. PanelApp is a collection of gene lists, with information about the evidence associated with variations in these genes. The goal […]... Read more »

  • October 14, 2015
  • 09:37 AM
  • 262 views

Video Tip of the Week: 100,000 Genomes Project

by Mary in OpenHelix

Software tools are certainly our focus for most of our tips of the week. But a key aspect of using the software and data repositories is that they rely on quality data. So sometimes we’ll highlight specific projects that will provide data to researchers, and this tip is one of those cases. Researchers should be […]... Read more »

  • October 7, 2015
  • 09:38 AM
  • 352 views

Video Tip of the Week: Weave, Web-based Analysis and Visualization Environment

by Mary in OpenHelix

At the recent Discovery On Target conference, a workshop on data and analytics for drug discovery contained several informative talks. This week’s Video Tip of the Week was inspired by the first speaker in that session, Georges Grinstein. Not only was the software he talked about something I wanted to examine right away (Weave)–his philosophy on […]... Read more »

Patterson, D., Hicks, T., Dufilie, A., Grinstein, G., & Plante, E. (2015) Dynamic Data Visualization with Weave and Brain Choropleths. PLOS ONE, 10(9). DOI: 10.1371/journal.pone.0139453  

Daniels, K., Grinstein, G., Russell, A., & Glidden, M. (2012) Properties of normalized radial visualizations. Information Visualization, 11(4), 273-300. DOI: 10.1177/1473871612439357  

  • September 30, 2015
  • 09:38 AM
  • 272 views

Video Tip of the Week: Global Biotic Interactions database, GloBI

by Mary in OpenHelix

And now for something completely different. Typically we highlight software that’s nucleotide or amino acid sequence related in some way. But this software is on a whole ‘nother level. It looks at interactions between species. This week we highlight GloBI, the Global Biotic Interactions database. Before you start thinking of Bambi and butterflies, though, consider […]... Read more »

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