All posts; Tags Include "Databases"
- August 26, 2010
- 04:55 PM
- 59 views
Galaxy, a stride towards reproducible computational research
Galaxy started out as a very useful tool to do genomics research that was reproducible and sharable. One of my pet peeves in reading research papers that use genomic analysis or online genomics resources is the materials and methods sections. Often the methods and parameters used are mentioned only in a very cursory manner, if [...]... 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
- August 20, 2010
- 04:10 PM
- 88 views
Genome-Scale Epigenetic Marker Detection Across Populations
by Michael Long in Phased
Lior Pachter (University of California at Berkeley, United States) and coworkers have developed MetMap software for uncovering epigenetic data hidden by standard MethylSeq analysis, which will advance our understanding of the role of epigenetics in human health and medicine. This news feature was written on August 20, 2010.... Read more »
Singer, M., Boffelli, D., Dhahbi, J., Schoenhuth, A., Schroth, G. P., Martin, D. I. K., & Pachter, L. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations. PLoS Computational Biology, 6(8). DOI: 10.1371/journal.pcbi.1000888
- July 27, 2010
- 11:17 AM
- 105 views
Twenty Million Papers in PubMed: A Triumph or a Tragedy?
by Duncan Hull in O'Really?
A quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it i... Read more »
Halevy, A., Norvig, P., & Pereira, F. (2009) The Unreasonable Effectiveness of Data. IEEE Intelligent Systems, 24(2), 8-12. DOI: 10.1109/MIS.2009.36
Torvik VI, & Smalheiser NR. (2009) Author Name Disambiguation in MEDLINE. ACM transactions on knowledge discovery from data, 3(3). PMID: 20072710
Islamaj Dogan R, Murray GC, Névéol A, & Lu Z. (2009) Understanding PubMed user search behavior through log analysis. Database : the journal of biological databases and curation. PMID: 20157491
- June 22, 2010
- 06:07 PM
- 146 views
Will Nano-Publications & Triplets Replace The Classic Journal Articles?
by Laika in Laika's Medliblog
“Libraries and journals articles as we know them will cease to exists” said Barend Mons at the symposium in honor of our Library 25th Anniversary (June 3rd). “Possibly we will have another kind of party in another 25 years”…. he continued, grinning. What he had to say the next half hour intrigued me. And although [...]... Read more »
van Haagen HH, 't Hoen PA, Botelho Bovo A, de Morrée A, van Mulligen EM, Chichester C, Kors JA, den Dunnen JT, van Ommen GJ, van der Maarel SM.... (2009) Novel protein-protein interactions inferred from literature context. PloS one, 4(11). PMID: 19924298
- April 28, 2010
- 09:00 AM
- 222 views
Peer-to-peer data storage
by David Bradley in Sciencetext
Whenever anyone mentions P2P file systems, the first thought that pops into the n00bs head is probably – piracy – and an image of teens downloading free copies of the latest young person’s popular music tracks from teh interwebs using an illicit file sharing system. Of course, Bit Torrent and other related systems can be [...]Post from: David Bradley's Sciencetext Tech TalkPeer-to-peer data storage
... Read more »
Yu-Wei Chan, Tsung-Hsuan Ho, Po-Chi Shih, & Yeh-Ching Chung. (2010) Malugo: A peer-to-peer storage system. Int. J. Ad Hoc and Ubiquitous Computing, 5(4), 209-218. info:/
- March 24, 2010
- 01:01 AM
- 252 views
Tip of the Week: Genomicus and genome evolution
Today’s tip is on Genomicus. Genomicus is a great tool to visualize gene duplication, synteny and genome evolution. The search and display interfaces are quite straightforward, and there are lots of great features (viewing ancestral gene information, links out to resources, different views of phylogenies, etc) in the tool. This video is only a short introduction. You can delve deeper into the tool with the help and documentation, including an 11 minute video.
There is also a recent (adva........ Read more »
Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics. DOI: 10.1093/bioinformatics/btq079
- February 12, 2010
- 10:12 AM
- 429 views
The 3rd OBO Foundry Workshop 2010, Cambridge, UK
by Duncan Hull in O'Really?
The Open Biomedical Ontologies (OBO) [1] are a set of reference ontologies for describing all kinds of biomedical data shared in a centralised OBO Foundry. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop two years [...]... Read more »
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C.... (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. DOI: 10.1038/nbt1346
- February 5, 2010
- 06:53 AM
- 478 views
Classic paper: Montagues and Capulets in Science
by Duncan Hull in O'Really?
In preparation for a joint seminar I’ll be doing with Midori Harris here at the EBI, here’s a classic paper [1,2] on the social problems of building biomedical ontologies. This paper is worth reading (or re-reading) because it makes lots of relevant points about the use and abuse of research and how people misunderstand each [...]... Read more »
Goble, C., & Wroe, C. (2004) The Montagues and the Capulets. Comparative and Functional Genomics, 5(8), 623-632. DOI: 10.1002/cfg.442
- February 5, 2010
- 02:37 AM
- 420 views
10 Websites With The Best Information on Depression
by Dr Shock in Dr Shock MD PhD
After searching for websites about depression (‘‘depression,’’ ‘‘depression treatment,’’ and ‘‘depression help’’) with a popular search engine: Google, the authors of this work carefully examined the websites. The websites were evaluated on accountability, interactivity, esthetics, readability and content quality. They also used the brief DISCERN as a content quality indicator for general consumers. They found [...]
Related posts:Assess Health Information Online Three........ Read more »
Zermatten, A., Khazaal, Y., Coquard, O., Chatton, A., & Bondolfi, G. (2010) Quality of web-based information on depression. Depression and Anxiety. DOI: 10.1002/da.20665
- December 29, 2009
- 01:43 AM
- 361 views
More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"
by Jonathan Eisen in The Tree of Life
Additional discussion of recent paper... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- December 14, 2009
- 10:30 AM
- 225 views
Errors in Biomedical Databases May Threaten Public Health
by Michael Long in Phased
Patricia Babbitt (University of California, San Francisco) and coworkers have found high error rates in three of four public databases of protein function, and offer recommendations on improving the accuracy and utility of these databases. This news feature was written on December 14, 2009.... Read more »
Schnoes, A. M., Brown, S. D., Dodevski, I., & Babbitt, P. C. (2009) Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies. PLoS Computational Biology, 5(12). DOI: 10.1371/journal.pcbi.1000605
- December 10, 2009
- 06:18 PM
- 557 views
The Semantic Biochemical Journal experiment
by Duncan Hull in O'Really?
There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and [...]... Read more »
Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009) Calling International Rescue: knowledge lost in literature and data landslide!. Biochemical Journal, 424(3), 317-333. DOI: 10.1042/BJ20091474
Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008) BioLit: integrating biological literature with databases. Nucleic Acids Research, 36(Web Server). DOI: 10.1093/nar/gkn317
Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000361
Pafilis, E., O'Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009) Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27(6), 508-510. DOI: 10.1038/nbt0609-508
Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009) Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10(Suppl 6). DOI: 10.1186/1471-2105-10-S6-S19
- October 23, 2009
- 02:31 AM
- 550 views
Wellcome to the Genome Campus
by Duncan Hull in O'Really?
So, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus.
The Genome Campus owes its existence to the [...]... Read more »
Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., & Ashburner, M. (2007) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research, 36(Database). DOI: 10.1093/nar/gkm791
- September 10, 2009
- 09:28 AM
- 739 views
Why don’t scientists share data?
by Duncan Hull in O'Really?
As Vince Smith once put it [1] data are the fuel of Science:
“The fabric of science is changing, driven by a revolution in digital technologies that facilitate the acquisition and communication of massive amounts of data. This is changing the nature of collaboration and expanding opportunities to participate in science. If digital technologies are the [...]... Read more »
Vince Smith. (2009) Data publication: towards a database of everything. BMC Research Notes, 2(1), 113. DOI: 10.1186/1756-0500-2-113
Anonymous. (2009) Data's shameful neglect: Research cannot flourish if data are not preserved and made accessible. Nature, 461(7261), 145-145. DOI: 10.1038/461145a
Schofield, P., Bubela, T., Weaver, T., Portilla, L., Brown, S., Hancock, J., Einhorn, D., Tocchini-Valentini, G., Hrabe de Angelis, M., & Rosenthal, N. (2009) Post-publication sharing of data and tools. Nature, 461(7261), 171-173. DOI: 10.1038/461171a
Toronto International Data Release Workshop Authors. (2009) Prepublication data sharing. Nature, 461(7261), 168-170. DOI: 10.1038/461168a
Bryn Nelson. (2009) Data sharing: Empty archives. Nature, 461(7261), 160-163. DOI: 10.1038/461160a
Michael Seringhaus, & Mark Gerstein. (2007) Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics, 8(1), 17. DOI: 10.1186/1471-2105-8-17
Duncan Hull, Steve Pettifer, & Douglas Kell. (2008) Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Computational Biology, 4(10). DOI: 10.1371/journal.pcbi.1000204
- July 6, 2009
- 02:43 AM
- 824 views
How and Why Junior Physicians use Web 2.0
by Dr Shock in Dr Shock MD PhD
The answers:
89% (32/35) of physicians used at least one Web 2.0 tool in their medical practice, with 80% (28/35) reporting the use of wikis, only one respondent contributed to web 2.0 making regular contribution to a medical wiki site
physicians checked for medical information on an average of 2.6 different sites a day, with 1.4 visits [...]... Read more »
Hughes, B., Joshi, I., Lemonde, H., & Wareham, J. (2009) Junior physician's use of Web 2.0 for information seeking and medical education: A qualitative study. International Journal of Medical Informatics. DOI: 10.1016/j.ijmedinf.2009.04.008
- November 26, 2008
- 12:00 AM
- 920 views
Neural Networking, Alzheimer's Disease and Memory Share a Few Things
by Amiya in Physiology physics woven fine
In the hippocampus, the part of brain that processes memory, has a neural architecture that resembles Hopfield network of artificial intelligence. This LAN like architecture is synchronized with cues from within the brain and outside. The brain thus has some similarities with information theory.... Read more »
E . Menschik. (2003) Neuromodulatory control of hippocampal function: towards a model of Alzheimer''s disease . . Artificial Intelligence in Medicine, 99-121.
E . Menschik. (2003) Neuromodulatory control of hippocampal function: towards a model of Alzheimer''s disease . . Artificial Intelligence in Medicine, 99-121.
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