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- October 31, 2012
- 09:35 AM
- 195 views
Video Tip of the Week: Integrative Multi-species Prediction (IMP) Network Analysis Resource
A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips: RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials for IMP are available from: http://t.co/zvlVmoph This week I have claimed Mary’s “collected” tip idea & will be featuring one of their [...]... Read more »
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, & Troyanskaya OG. (2012) IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. DOI: 10.1093/nar/gks458
- September 26, 2012
- 09:32 AM
- 221 views
Video Tip of the Week: 1000 Genomes Dataset Browser from NCBI
A recent NCBI Newsletter announced the release of a new resource named the 1000 Genomes Dataset Browser, and that is the resource that I will be featuring in this tip. It is one of the tools available through the new NCBI Variation resources page, which also features resources such as dbSNP, dbVar, dbGaP and ClinVar (many [...]... Read more »
The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 1061-1073. DOI: 10.1038/nature09534
- August 27, 2012
- 09:26 AM
- 197 views
Enjoying the 2012 NAR Web Server Issue & a Cup of Coffee
In hunting for something to feature for this week’s tip, I noticed that Nucleic Acids Research had released their 2012 Web Server Issue back in July. As many of you are might be aware, the Nucleic Acids Research journal is a forum where developers can present computational biology papers that describe the development of biologically relevant algorithms, novel usage [...]... Read more »
Gary Benson. (2012) Editorial: NUCLEIC ACIDS RESEARCH ANNUAL WEB SERVER ISSUE IN 2012 . Nucleic Acids Research, 40(W1). DOI: 10.1093/nar/gks607
Michelle D. Brazas, David Yim, Winston Yeung, & B. F. Francis Ouellette. (2012) A decade of web server updates at the bioinformatics links directory: 2003–2012. Nucleic Acids Research, 40(W1). DOI: 10.1093/nar/gks632
- August 1, 2012
- 08:52 AM
- 285 views
Video Tip of the Week: Microbiome Resources From JGI
Just over a month ago an issue of Nature had two articles from the Human Microbiome Project Consortium – you may have seen them, or noticed the Friday SNPets items we had on them. I promised myself that I’d read the articles (which I did), and that I’d visit my old friends the IMG (Integrated [...]... Read more »
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann.... (2012) IMG/M: the integrated metagenome data management and comparative analysis system. Nucl. Acids Res. . DOI: 10.1093/nar/gkr975
Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams.... (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucl. Acids Res. DOI: 10.1093/nar/gkr1044
- July 16, 2012
- 12:59 PM
- 277 views
More Big Data to Consider: Bioimage Informatics
I’m not sure any more when I signed up for complementary copies of Nature Methods, but just like clockwork my copy arrives each month. If you’d like to get it too, you can apply for a subscription here (Firefox seems to work better than IE, btw). This month’s issue particularly interested me because it contains a focus on Bioimage Informatics. [...]... Read more »
Greg Miller. (2012) Blast Injuries Linked to Neurodegeneration in Veterans. Science, 336(6083), 790-791. DOI: 10.1126/science.336.6083.790
Gene Myers. (2012) Why bioimage informatics matters. Nature Methods, 659-660. DOI: 10.1038/nmeth.2024
Anne E Carpenter, Lee Kamentsky, & Kevin W Eliceiri. (2012) A call for bioimaging software usability. Nature Methods 9, 666-670. DOI: 10.1038/nmeth.2073
Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam.... (2012) Biological imaging software tools. Nature Methods, 697-710. DOI: 10.1038/nmeth.2084
- June 27, 2012
- 09:03 AM
- 366 views
Video Tip of the Week: The PSI SBKB’s New Content Hubs
In today’s tip I will feature the newly organized content hubs over at the Protein Structure Initiative’s Structural Biology Knowledgebase, or PSI SBKB. We do have a free, full-length tutorial on the PSI SBKB that we are in the process of updating, but I thought I’d just touch on one of the new updates to [...]... Read more »
Gifford LK, Carter LG, Gabanyi MJ, Berman HM, & Adams PD. (2012) The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. Journal of structural and functional genomics, 13(2), 57-62. PMID: 22527514
Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA.... (2011) The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, 12(2), 45-54. PMID: 21472436
Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, & LaBaer J. (2011) PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. Journal of structural and functional genomics, 12(2), 55-62. PMID: 21360289
- May 23, 2012
- 08:49 AM
- 453 views
Video Tip of the Week: the New PubMed Filters Sidebar
In today’s tip I am linking to a YouTube video from NCBI that briefly explains the new Filters Sidebar feature that has been added to PubMed. We first saw a tweet that the change was coming back on May 2nd, just as I was completing a total update to our full PubMed tutorial*. I struggled with [...]... Read more »
Sayers E. W., Barrett T., Benson D. A., Bolton E., Bryant S. H., Canese K., Chetvernin V., Church D. M., DiCuccio M., & Federhen S. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr1184
- April 18, 2012
- 10:00 AM
- 423 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. The Cell Image Library is brought to you by the The American Society for Cell Biology (ASCB), and contains thousands of images, time series and groups of images, videos and animations of cells in a variety of ........ Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- April 18, 2012
- 09:10 AM
- 355 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. [...]... Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- March 14, 2012
- 09:40 AM
- 415 views
Video Tip of the Week: New Genetic Testing Registry (GTR) Resource
For more information, see our blog post at http://blog.openhelix.eu/?p=11439. In this movie we compare the new GTR resource from NCBI to other clinical resources that you may already be using, to answer why you may want to use the GTR.... Read more »
Pagon RA. (2006) GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94(3), 343-8. PMID: 16888670
Mitchell JA, Fomous C, & Fun J. (2006) Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94(3), 336-42. PMID: 16888669
Amberger, J., Bocchini, C., & Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Human Mutation, 32(5), 564-567. DOI: 10.1002/humu.21466
Aymé, S., & Schmidtke, J. (2007) Networking for rare diseases: a necessity for Europe. Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 50(12), 1477-1483. DOI: 10.1007/s00103-007-0381-9
- February 22, 2012
- 10:09 AM
- 649 views
Video tip of the week: Updated Introductory Tutorial on the RCSB PDB
This post is part of OpenHelix's "Tip of the Week" blog feature. For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. ... Read more »
Berman, H., & et al. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
- January 18, 2012
- 09:00 AM
- 525 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
- 782 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 14, 2011
- 09:05 AM
- 3,308 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
- November 9, 2011
- 09:06 AM
- 901 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
- October 31, 2011
- 06:17 PM
- 671 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
- 701 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 5, 2011
- 08:34 AM
- 817 views
Tip of the Week: VnD Resource for Genetic Variation and Drug Information (with video)
In today’s tip I am going to feature a resource that I found recently. I’ve been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutorial, which is sponsored by the RCSB PDB team. I have therefore been thinking about protein structures and small [...]... Read more »
Yang, J., Oh, S., Ko, G., Park, S., Kim, W., Lee, B., & Lee, S. (2010) VnD: a structure-centric database of disease-related SNPs and drugs. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq957
- August 31, 2011
- 09:02 AM
- 1,153 views
Tip of the Week: From UniProt to the PSI SBKB and Back Again
It is often beneficial to visit multiple biomedical databases or resources, even if they seem to provide overlapping information because no two resources focus on the exact same information, or present it in exactly the same way. Instead of duplicating each others’ curation efforts, database often link out to related information at other resources. You [...]... Read more »
The UniProt Consortium. (2009) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp846
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L.... (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn790
- July 27, 2011
- 09:18 AM
- 1,323 views
Tip of the Week: the New SIB Bioinformatics Resource Portal
A few years ago I did a tip on the proteomic tools list available from the ExPASy site. You can still get to that list, but it is no longer being updated. Instead the entire ExPASy site has been updated and reorganized and is now the new Swiss Institute of Bioinformatics (SIB) Bioinformatics Resource Portal. [...]... Read more »
Gasteiger, E. (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784-3788. DOI: 10.1093/nar/gkg563
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