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  • November 25, 2015
  • 09:50 AM

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

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

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

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

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

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

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

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

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  

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