118 posts · 71,256 views
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.
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- February 1, 2012
- 09:30 AM
- 63 views
Video Tip of the Week: SNPeffect 4.0
One of the most frequent questions we hear when we do workshops is: how to I find out if this SNP has an effect on my favorite protein? Well, that’s assuming it is a coding SNP. Of course, promoter SNPs and splicing SNPs and other features would be great to assess as well. Right now, though, the most mature tools are those that look at the effects of variation on the coding of the amino acids in proteins.... Read more »
De Baets, G., Van Durme, J., Reumers, J., Maurer-Stroh, S., Vanhee, P., Dopazo, J., Schymkowitz, J., & Rousseau, F. (2011) SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr996
- January 25, 2012
- 10:09 AM
- 29 views
Video Tip of the Week: Biological Sequence Analysis I @ NIH
Well, more than a tip, a lecture. We haven’t done a tip today, we are in grant application process (time limiting) and this is an excellent video we’d like for more to see. Mary posted the first lecture, The Genomic Landscape circa 2012, in a series given at NIH. As the course description mentions, “The lectures [...]... Read more »
Green, E., Guyer, M., Green, E., Guyer, M., Manolio, T., & Peterson, J. (2011) Charting a course for genomic medicine from base pairs to bedside. Nature, 470(7333), 204-213. DOI: 10.1038/nature09764
- January 23, 2012
- 10:15 AM
- 103 views
The Genomics Landscape circa 2012 lecture by Eric Green (with video)
There is a course running right now at NHGRI that is covering a timely set of genomics aspects. Called Current Topics in Genome Analysis 2012 (CTGA), it’s going to hit a great series of aspects of the current landscape–and offer a look at the future–in genomics.
On the course page you can download the slides, and watch the YouTube videos of the lecture. I had a chance to watch the first one so far, and I’ll summarize it below. But be sure to check back to the Genome.go........ Read more »
Green, E., Guyer, M., Green, E., Guyer, M., Manolio, T., & Peterson, J. (2011) Charting a course for genomic medicine from base pairs to bedside. Nature, 470(7333), 204-213. DOI: 10.1038/nature09764
- January 18, 2012
- 09:00 AM
- 94 views
Video tip of the week: OpenHelix App on SciVerse to Extend Research
In today’s tip I will introduce you to another one of our efforts to “extend research” by showing you a glimpse of an OpenHelix app that we designed for the SciVerse platform from Elsevier. This app scans a ScienceDirect journal article for any database names or URLs that we train on, and then displays a list of such resources in the window of the app.... Read more »
Mortensen, H., & Euling, S. (2011) Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century. Toxicology and Applied Pharmacology. DOI: 10.1016/j.taap.2011.01.015
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
Bengtson, J. (2011) ScienceDirect Through SciVerse: A New Way To Approach Elsevier. Medical Reference Services Quarterly, 30(1), 42-49. DOI: 10.1080/02763869.2011.541346
- January 11, 2012
- 10:00 AM
- 138 views
Video tip of the week: Functional Glycomics Gateway
by Mary Mangan in OpenHelix
This week’s tip is on our newest tutorial suite on the Functional Glycomics Gateway. It is freely available to everyone because it is sponsored by the Consortium for Functional Glycomics. From the suite landing page, click on the “Launch Online Tutorial” button to view the movie.... Read more »
Raman, R., Raguram, S., Venkataraman, G., Paulson, J., & Sasisekharan, R. (2005) Glycomics: an integrated systems approach to structure-function relationships of glycans. Nature Methods, 2(11), 817-824. DOI: 10.1038/nmeth807
Raman, R., Venkataraman, M., Ramakrishnan, S., Lang, W., Raguram, S., & Sasisekharan, S. (2006) Advancing glycomics: Implementation strategies at the Consortium for Functional Glycomics. Glycobiology, 16(5), 82-90. DOI: 10.1093/glycob/cwj080
Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, & Etzler ME. (2009) Essentials of Glycobiology, 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. PMID: 20301239
- December 21, 2011
- 10:15 AM
- 235 views
Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes)
Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December.
Oh, that’s not what this tip is about, it’s about database of orthologous groups of genes, eggNOG. We’ve mentioned eggNOG before several times, but only in passing or in relation (orthologous?........ Read more »
Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T.... (2011) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. DOI: 10.1093/nar/gkr1060
- December 19, 2011
- 11:30 AM
- 107 views
Got a genome transcriptome. Now what?
I was catching up on some mailing list reading last week when I saw an unusual item come across the UCSC discussion mailing list. Someone who is in the process of obtaining genome and transcriptome sequence for a new project asked the UCSC group for guidance on what to do with it. It’s actually a [...]... Read more »
Xu, X., Nagarajan, H., Lewis, N., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S.... (2011) The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, 29(8), 735-741. DOI: 10.1038/nbt.1932
Klimke, W., O'Donovan, C., White, O., Brister, J., Clark, K., Fedorov, B., Mizrachi, I., Pruitt, K., & Tatusova, T. (2011) Solving the Problem: Genome Annotation Standards before the Data Deluge. Standards in Genomic Sciences, 5(1), 168-193. DOI: 10.4056/sigs.2084864
- December 19, 2011
- 11:30 AM
- 192 views
Got a genome and transcriptome. Now what?
I was catching up on some mailing list reading last week when I saw an unusual item come across the UCSC discussion mailing list. Someone who is in the process of obtaining genome and transcriptome sequence for a new project asked the UCSC group for guidance on what to do with it. It’s actually a question we’ve been hearing a lot in workshops–people are considering grants for this sort of project, or have plans for a brand new sequencer that’s arrived at their site. I thought other peopl........ Read more »
Xu, X., Nagarajan, H., Lewis, N., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S.... (2011) The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, 29(8), 735-741. DOI: 10.1038/nbt.1932
Klimke, W., O'Donovan, C., White, O., Brister, J., Clark, K., Fedorov, B., Mizrachi, I., Pruitt, K., & Tatusova, T. (2011) Solving the Problem: Genome Annotation Standards before the Data Deluge. Standards in Genomic Sciences, 5(1), 168-193. DOI: 10.4056/sigs.2084864
- December 14, 2011
- 09:05 AM
- 520 views
Video Tip of the Week: Big Changes to NCBI’s Genome Resources
NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been [...]... Read more »
Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999) Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics, 15(7), 536-543. DOI: 10.1093/bioinformatics/15.7.536
Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T.... (2011) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Research. DOI: 10.1093/nar/gkr1163
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S.... (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. DOI: 10.1093/nar/gkr1184
- December 12, 2011
- 10:40 AM
- 519 views
Why don’t users employ workflows for “big data”? I know why.
Yesterday a tweet to a great post came across the ethers, and ever since I read it I knew I had to write this post. Here’s the original nugget:
RT @ctitusbrown: (my) thoughts on data intensive science & workflows: http://bit.ly/tWXSnx
It is a post about why end users are not adopting workflows which could really help them in this eScience world we find ourselves in, and as we keep moving forward with giant data sets and “big data” projects. And some other points about........ Read more »
Goecks, J., Nekrutenko, A., Taylor, J., & Galaxy Team, T. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8). DOI: 10.1186/gb-2010-11-8-r86
- December 7, 2011
- 09:34 AM
- 215 views
Video tip of the week: VarSifter for identifying key sequence variations
Recently many of the bioinformatics tweeps I follow were excited about the tool called VarSifter. Here’s the notice that I saw: RT @yokofakun: http://www.youtube.com/watch?v=I7azpqTWFuM Jamie Teer describes VarSifter, an interactive GUI tool for handing/quering/filtering VCFs #ngs I just had a chance to watch the video, and now I can see why they were impressed! Over [...]... Read more »
Robinson, J., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E., Getz, G., & Mesirov, J. (2011) Integrative genomics viewer. Nature Biotechnology, 29(1), 24-26. DOI: 10.1038/nbt.1754
Dreszer, T., Karolchik, D., Zweig, A., Hinrichs, A., Raney, B., Kuhn, R., Meyer, L., Wong, M., Sloan, C., Rosenbloom, K.... (2011) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research. DOI: 10.1093/nar/gkr1055
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & , . (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. DOI: 10.1093/bioinformatics/btp352
- November 30, 2011
- 08:25 AM
- 254 views
Video Tip of the Week: Phosida, a post-translational modification database
Over 2 years ago I did a tip of the week on Phosida. Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools (prediction and [...]... Read more »
Gnad, F., Gunawardena, J., & Mann, M. (2010) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1159
- November 23, 2011
- 09:24 AM
- 297 views
Video Tip of the Week: BioMart’s new central portal
BioMart is widely-used data management open-source software, with an interface that enables end-users to generate complex and customized queries across many types and sources of biological data. It’s part of the GMOD tool kit, and many project teams that have big data have chosen the BioMart software to organize and make their data available to [...]... Read more »
Kasprzyk, A. (2011) BioMart: driving a paradigm change in biological data management. Database. DOI: 10.1093/database/bar049
Zhang, J., Haider, S., Baran, J., Cros, A., Guberman, J., Hsu, J., Liang, Y., Yao, L., & Kasprzyk, A. (2011) BioMart: a data federation framework for large collaborative projects. Database. DOI: 10.1093/database/bar038
Guberman, J., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R.... (2011) BioMart Central Portal: an open database network for the biological community. Database. DOI: 10.1093/database/bar041
Haider, S., Ballester, B., Smedley, D., Zhang, J., Rice, P., & Kasprzyk, A. (2009) BioMart Central Portal--unified access to biological data. Nucleic Acids Research, 37(Web Server). DOI: 10.1093/nar/gkp265
- November 16, 2011
- 08:09 AM
- 335 views
Video Tip of the Week: MapMi, automated mapping of microRNA loci
Today’s video tip of the week is on MapMi. This tool is found at EBI and was developed by the Enright lab. The purpose of this tool is a computational system for mapping of miRNAs within and across species. As the abstract of their recent paper says: Currently miRBase is their primary repository, providing annotations [...]... Read more »
Guerra-Assuncao, J., & Enright, A. (2010) MapMi: automated mapping of microRNA loci. BMC Bioinformatics, 11(1), 133. DOI: 10.1186/1471-2105-11-133
- November 9, 2011
- 09:06 AM
- 334 views
Video Tip of the Week: The New Database of Genomic Variants – DGV2
In today’s tip I will briefly introduce you to the beta version of the updated DGV resource. The Database of Genomic Variants, or DGV, was created in 2004 at a time early in the understanding of human structural variation, or SV, which is defined by DGV as genomic variation larger than 50bp. DGV has historically [...]... Read more »
Church, D., Lappalainen, I., Sneddon, T., Hinton, J., Maguire, M., Lopez, J., Garner, J., Paschall, J., DiCuccio, M., Yaschenko, E.... (2010) Public data archives for genomic structural variation. Nature Genetics, 42(10), 813-814. DOI: 10.1038/ng1010-813
- November 7, 2011
- 11:32 AM
- 274 views
Getting help with bioinformatics questions online
There are thousands of bioinformatics databases, servers, algorithms, and apps in the bioinformatics ecosystem. Even though we are immersed in this environment ourselves, it seems that every day there’s something new, and in every workshop we do someone brings us an issue they have which requires some sort of tool that we haven’t explored yet–some [...]... 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
Dall'Olio, G., Marino, J., Schubert, M., Keys, K., Stefan, M., Gillespie, C., Poulain, P., Shameer, K., Sugar, R., Invergo, B.... (2011) Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology, 7(9). DOI: 10.1371/journal.pcbi.1002202
- November 2, 2011
- 09:20 AM
- 322 views
Video Tip of the Week: MizBee Synteny Browser
In my last tip of the week I was really pleased about the opportunity to see the data from a paper set up in a custom GBrowse, but it also reminded me of the limitations of some current strategies for visualization that we are facing. In that case one of the things that I wanted [...]... Read more »
Meyer, M., Munzner, T., & Pfister, H. (2009) MizBee: A Multiscale Synteny Browser. IEEE Transactions on Visualization and Computer Graphics, 15(6), 897-904. DOI: 10.1109/TVCG.2009.167
Meyer, M., Munzner, T., DePace, A., & Pfister, H. (2010) MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data. IEEE Transactions on Visualization and Computer Graphics, 16(6), 908-917. DOI: 10.1109/TVCG.2010.137
Meyer, M., Wong, B., Styczynski, M., Munzner, T., & Pfister, H. (2010) Pathline: A Tool For Comparative Functional Genomics. Computer Graphics Forum, 29(3), 1043-1052. DOI: 10.1111/j.1467-8659.2009.01710.x
- October 31, 2011
- 06:17 PM
- 181 views
On a Mission for Protein Information
It’s probably just the human brain’s ability to connect dots & find patterns, but it can be interesting how many “unrelated” events and information bits accumulate in my head & eventually get mulled into an idea or theory. Take, for example, a recent biotech mixer, bits from an education leadership series & a past Nature [...]... Read more »
Sierpinski P, Garrett J, Ma J, Apel P, Klorig D, Smith T, Koman LA, Atala A, & Van Dyke M. (2008) The use of keratin biomaterials derived from human hair for the promotion of rapid regeneration of peripheral nerves. Biomaterials, 29(1), 118-28. PMID: 17919720
Edwards, A., Isserlin, R., Bader, G., Frye, S., Willson, T., & Yu, F. (2011) Too many roads not taken. Nature, 470(7333), 163-165. DOI: 10.1038/470163a
- October 26, 2011
- 09:03 AM
- 311 views
Video Tip of the Week: Variation Data from Ensembl
Trey introduced me to this “decent collection of video tutorials ” from Ensembl, but he and Mary are currently in Morocco teaching a 3-day bioinformatics workshop & then attending the conference (yes, I am envious!). I am therefore creating this week’s tip based on the tutorials that Trey pointed me to. In today’s tip I am [...]... Read more »
Flicek, P., Aken, B., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S.... (2009) Ensembl's 10th year. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp972
- October 19, 2011
- 09:17 AM
- 330 views
Video Tip of the Week: Mitochondrial transcriptome GBrowser
Subtitled: the data is not in the papers anymore. Again. And again. As the data deluge continues, and those next-gen sequencing setups and labs continue to crank out more and more data, the details cannot be captured in the papers anymore. They just can’t. Authors can summarize the key findings, and show compelling examples and [...]... Read more »
Mercer, T., Neph, S., Dinger, M., Crawford, J., Smith, M., Shearwood, A., Haugen, E., Bracken, C., Rackham, O., Stamatoyannopoulos, J.... (2011) The Human Mitochondrial Transcriptome. Cell, 146(4), 645-658. DOI: 10.1016/j.cell.2011.06.051
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