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  • October 7, 2015
  • 09:38 AM

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

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 »

  • September 23, 2015
  • 09:39 AM

Video Tip of the Week: UCSC Xena System for functional and cancer genomics

by Mary in OpenHelix

When we go out and do workshops, we get a lot of requests from researchers who would like some guidance on cancer genomics tools. Our particular mission has been to aim more broadly at tools that are of wide interest and not to focus on a particular disease or condition area. But certainly the cancer […]... Read more »

Cline, M., Craft, B., Swatloski, T., Goldman, M., Ma, S., Haussler, D., & Zhu, J. (2013) Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser. Scientific Reports. DOI: 10.1038/srep02652  

Cheng PF, Dummer R, & Levesque MP. (2015) Data mining The Cancer Genome Atlas in the era of precision cancer medicine. Swiss Med Wkly. info:/10.4414/smw.2015.14183

  • September 17, 2015
  • 09:03 AM

What’s the Answer? (building the ultimate bioinformatics resource)

by Mary in OpenHelix

This week’s highlighted item will apparently answer all the questions in the future, rendering my weekly foray moot. Ok, kidding aside, I think this is a great idea. A sort of “living” better-than-textbook project that will really be the only way to keep up with a field that changes as fast as bioinformatics does. If they […]... Read more »

Parnell, L., Lindenbaum, P., Shameer, K., Dall'Olio, G., Swan, D., Jensen, L., Cockell, S., Pedersen, B., Mangan, M., Miller, C.... (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216  

  • September 16, 2015
  • 09:37 AM

Video Tip of the Week: BANDAGE for visualization of de novo assembly graphs

by Mary in OpenHelix

Typically we highlight web-based tools for our Tips of the Week. But sometimes there’s a tool that has some novel visualizations that we want to note that might require a user to do a download and installation. This week’s tool is one of those–BANDAGE, a Bioinformatics Application for Navigating De novo Assembly Graphs Easily. I heard […]... Read more »

  • September 9, 2015
  • 09:36 AM

Video Tip of the Week: UCSC features for ENCODE data utilization

by Mary in OpenHelix

As noted in last week’s tip about the ENCODE DCC at Stanford, there was a workshop recently for the ENCODE project. There were a lot of folks speaking and a big room full of attendees. You should check out the full agenda and the playlist at the NHGRI site for all the videos, slides, and […]... Read more »

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  

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  

Raney, B., Dreszer, T., Barber, G., Clawson, H., Fujita, P., Wang, T., Nguyen, N., Paten, B., Zweig, A., Karolchik, D.... (2013) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics, 30(7), 1003-1005. DOI: 10.1093/bioinformatics/btt637  

  • September 2, 2015
  • 09:36 AM

Video Tip of the Week: ENCODE Data Coordination Center, phase 3

by Mary in OpenHelix

The ENCODE project began many years ago, with a pilot phase, that examined just 1% of the human genome. But this initial exploration helped the consortium participants to iron out some of the directions for later stages–including focusing on specific cell lines, techniques, and technologies in Phase 2. There have been a number of publications […]... Read more »

Malladi, V., Erickson, D., Podduturi, N., Rowe, L., Chan, E., Davidson, J., Hitz, B., Ho, M., Lee, B., Miyasato, S.... (2015) Ontology application and use at the ENCODE DCC. Database. DOI: 10.1093/database/bav010  

  • August 26, 2015
  • 09:40 AM

Video Tip of the Week: Human Metabolome Database, HMDB

by Mary in OpenHelix

The HMDB, or Human Metabolome DataBase, is another nice data collection and tools from the Wishart lab. Although we have mentioned it in the past, because of it’s emphasis more on small molecules it isn’t something we covered in detail. But with this new video that’s available, I thought it was a good time to […]... Read more »

Wishart, D., Jewison, T., Guo, A., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E.... (2012) HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Research, 41(D1). DOI: 10.1093/nar/gks1065  

  • August 19, 2015
  • 09:40 AM

Video Tip of the Week: gene.iobio for genome and variation browsing

by Mary in OpenHelix

Twitter erupted recently with some chatter about a new tool that people seemed to really like. The iobio team from the Marth lab had launched a new gene “app” on their iobio framework. Here was some of the response: Slick! Gene.iobio tool to interactively examine #genetic variants in patient sample #genomics — Julie […]... Read more »

Miller, C., Qiao, Y., DiSera, T., D'Astous, B., & Marth, G. (2014) bam.iobio: a web-based, real-time, sequence alignment file inspector. Nature Methods, 11(12), 1189-1189. DOI: 10.1038/nmeth.3174  

  • August 12, 2015
  • 09:41 AM

Video Tip of the Week: World Tour of Genomics Resources, part II

by Mary in OpenHelix

This week’s tip is not our usual short video. We’ll connect you to our newest tutorial suite, our World Tour of Genomics Resources, part II. Our previous tour was really popular–because as much as bench researchers know about the tools they currently use–everyone realizes there are more tools out there. And many of them don’t […]... Read more »

Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010) OpenHelix: bioinformatics education outside of a different box. Briefings in Bioinformatics, 11(6), 598-609. DOI: 10.1093/bib/bbq026  

  • August 5, 2015
  • 09:38 AM

Video Tip of the Week: Araport, Arabidopsis Portal

by Mary in OpenHelix

The recent Plant Biology 2015 conference tweets were full of delightful morsels (#plantbiology15). Some of them edible. I am very psyched to learn of the Legume Federation. Legumes are *way* at the top of my list of favorite organisms. I think it was their tweet of the Araport data that led to this week’s video tip […]... Read more »

Hanlon, M., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E.... (2015) Araport: an application platform for data discovery. Concurrency and Computation: Practice and Experience. DOI: 10.1002/cpe.3542  

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  

  • July 29, 2015
  • 09:39 AM

Video Tip of the Week: PathWhiz for Pathways, Part II

by Mary in OpenHelix

This week’s tip is a follow-up to the PathWhiz one featured last week. After I had finished writing that one, the second video in the series became available. It has a lot more detail on how to work with the tool. I’m not going to go into the introduction here again, you can flip back […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • July 22, 2015
  • 09:36 AM

Video Tip of the Week: PathWhiz for graphical appeal and computational readability

by Mary in OpenHelix

“Pathway diagrams are the road maps of biology.” This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announced. The NAR database issue in January and the mid-year web server issue are perfectly timed items that I can content […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • July 15, 2015
  • 09:39 AM

Video Tip of the Week: Introduction to the UCSC Genome Browser

by Mary in OpenHelix

This week’s tip is quite multi-media. There’s a video, as required. But there’s a traditional published paper format, too. And there’s also the free training slides and exercises from us, sponsored by the folks who create the UCSC Genome Browser. So if you prefer audio, graphics, or text–we’ve got it all in this week’s tip. […]... Read more »

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  

  • July 8, 2015
  • 09:45 AM

Video Tip of the Week: PhenomeCentral

by Mary in OpenHelix

Silos. This is a big problem for us with human genome data from individuals. We’re getting sequences, but they are locked up in various ways. David Haussler’s talk at the recent Global Alliance for Genomics and Health meeting (GA4GH) emphasized this barrier, and also talked about ways they are looking to work around the legal, […]... Read more »

Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M., Ray, P.... (2013) PhenoTips: Patient Phenotyping Software for Clinical and Research Use. Human Mutation, 34(8), 1057-1065. DOI: 10.1002/humu.22347  

  • July 1, 2015
  • 09:39 AM

Video Tip of the Week: MorphoGraphX, morphogenesis in 4D

by Mary in OpenHelix

This week’s Video Tip of the Week covers a different aspect of bioinformatics than some of our other tips. But having been trained as a cell biologist, I do consider imaging software as an important part of the crucial software ecosystem. Also, since it’s a holiday week and traffic may be light in the US, […]... Read more »

Barbier de Reuille, P., Routier-Kierzkowska, A., Kierzkowski, D., Bassel, G., Schüpbach, T., Tauriello, G., Bajpai, N., Strauss, S., Weber, A., Kiss, A.... (2015) MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife. DOI: 10.7554/eLife.05864  

  • June 24, 2015
  • 10:30 AM

Video Tip of the Week: handy way to make citations quickly

by Mary in OpenHelix

This is not a typical tip–where we explore the features and details of bioinformatics tools. But it’s one of those handy little features that may make your life easier. It’s made mine better lately. I had been using the ScienceSeeker citation generator system for creating citations that would then aggregate to either ScienceSeeker or ResearchBlogging. But ScienceSeeker’s model recently changed. And ResearchBlogging’s support and stability is…well, uneven.... Read more »

  • June 17, 2015
  • 09:38 AM

Video Tip of the Week: ZBrowse for GWAS viewing and exploration

by Mary in OpenHelix

Maybe you’ve heard of the others. ABrowse. BBrowse. CBrowse. [you get the idea] GBrowse has been widely adopted. JBrowse is picking up steam. Into the orderly arrangement we now throw ZBrowse: a new way to look at genome-wide association study data. Sharing and chatter about ZBrowse for viewing GWAS was abundant when the paper was […]... Read more »

  • June 11, 2015
  • 09:35 AM

What’s the Answer? (pan-genome graphs)

by Mary in OpenHelix

This weeks highlighted discussion is the problem of pan-genome graphs, which are ways to represent the variation we find in genomes instead of a linear reference sequence view. I was really struggling with these concepts until I heard a talk at the #TRICON meeting recently. David Haussler had some really helpful visuals. I don’t have […]... Read more »

Benedict Paten, Adam Novak, & David Haussler. (2014) Mapping to a Reference Genome Structure. arXiv: 1404.5010v1

Nguyen, N., Hickey, G., Zerbino, D., Raney, B., Earl, D., Armstrong, J., Kent, W., Haussler, D., & Paten, B. (2015) Building a Pan-Genome Reference for a Population. Journal of Computational Biology, 22(5), 387-401. DOI: 10.1089/cmb.2014.0146  

  • June 10, 2015
  • 09:36 AM

Video Tip of the Week: GenomeConnect, the ClinGen piece for patients

by Mary in OpenHelix

GenomeConnect is part of the larger ClinGen effort that I began to discuss last week, but this aspect is specifically a portal for patients who have (or may get) genetic testing results of various types. The ClinGen team will use this interface to capture the testing data–the genotypes, and the health history, or phenotypes, and […]... Read more »

Rehm, H., Berg, J., Brooks, L., Bustamante, C., Evans, J., Landrum, M., Ledbetter, D., Maglott, D., Martin, C., Nussbaum, R.... (2015) ClinGen — The Clinical Genome Resource. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMsr1406261  

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