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OpenHelix
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- January 18, 2012
- 09:00 AM
- 99 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
- 142 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
- 535 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
- 339 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
- 182 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
- 316 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
- 392 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
- 522 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
- 585 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
- May 18, 2011
- 08:47 AM
- 611 views
Tip of the Week: Allen Institute’s Brain Explorer
Not that long ago Mary posted on updates that occurred recently at the Allen Institute for Brain Science & hinted that there might be a tip coming about their cool 3D Brain Explorer tool – well, today’s the day! As Mary mentions in her post, the Allen Institute has created some phenomenal tools and detailed datasets for brain
From the Brain Explorer documentation, the Explorer allows users to:
# View a fully interactive version of the Allen Human Brain Atlas in 3D for two donors.
........ Read more »
Lau, C., Ng, L., Thompson, C., Pathak, S., Kuan, L., Jones, A., & Hawrylycz, M. (2008) Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain. BMC Bioinformatics, 9(1), 153. DOI: 10.1186/1471-2105-9-153
- April 27, 2011
- 12:43 PM
- 713 views
Sage Bioinformatics Advice, But…
Bioinformatics analysis is a powerful technique applicable to a wide variety of fields, and the subject of many a blog post here at OpenHelix. I’ve had two particular bioinformatics articles on my desk for a couple of months now, waiting for me to be able to articulate my thoughts on them. They both offer great [...]... Read more »
Cline, M., & Karchin, R. (2010) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics, 27(4), 441-448. DOI: 10.1093/bioinformatics/btq695
Vincent Shen. (2011) Mistaken identities in proteomics. BioTechniques. info:other/http://www.biotechniques.com/news/biotechniquesNews/biotechniques-312015.html
- April 13, 2011
- 09:16 AM
- 451 views
Tip of the week: VirusMINT
In this week’s tip I’d like to introduce you to VirusMINT. We found VirusMINT during our ‘regularly scheduled’ update of our Introductory tutorial on MINT, or the Molecular INTeraction database. We really like MINT for all the great interaction information they provide on a wide variety of species. When we saw they had a ‘virally focused’ database, we had to check it out.
It turns out that VirusMINT is really unique in that it shows interactions BETWEEN human........ Read more »
Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M.... (2009) VirusMINT: a viral protein interaction database. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn739
Chatr-aryamontri, A., Ceol, A., Palazzi, L., Nardelli, G., Schneider, M., Castagnoli, L., & Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Research, 35(Database). DOI: 10.1093/nar/gkl950
Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L., & Cesareni, G. (2009) MINT, the molecular interaction database: 2009 update. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp983
- March 28, 2011
- 09:15 AM
- 730 views
Protein Structure Analysis – How Far We’ve Come!
The team here at OpenHelix has recently updated our sponsored tutorials on two excellent structural biology resources, the RCSB Protein Data Bank (PBD) and the PSI-Nature Structural Biology Knowledgebase (PSI SBKB). Because the tutorials are sponsored by these resources they are free for anyone to view and download in full. You can access our training materials for the resources at our RCSB PDB landing page, or our PSI SBKB landing page. I’m very happy with both tutorial suites, so please........ Read more »
Berman, H. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
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
Doolittle, R. (2010) The Roots of Bioinformatics in Protein Evolution. PLoS Computational Biology, 6(7). DOI: 10.1371/journal.pcbi.1000875
Miller, M. (2010) The early years of retroviral protease crystal structures. Biopolymers, 94(4), 521-529. DOI: 10.1002/bip.21387
- March 9, 2011
- 09:15 AM
- 536 views
Tip of the Week: World Tour of Genomics Resources
Most weeks our tip is a five-minute movie that quickly introduces you to a new resource, or a cool new function at an established resource. Occasionally we feature one of our full resource tutorial that is being made freely available through resource sponsorship of our training suite. In this week’s tip we provide access to one of our tutorials that is especially near and dear to our heart. It is a World Tour of Genomics Resources in which we explore a variety of publicly-available biomedi........ 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
- February 2, 2011
- 09:05 AM
- 647 views
Tip of the Week: RCSB PDB Data Distribution Summaries
In today’s tip I will feature the data distribution summaries and their drill down features which you can see from many RCSB PDB searches. We are in the process of updating our full tutorial sponsored by the RCSB PDB team, and as part of that effort I’ve gotten to know and appreciate this new data presentation format. Over the last five years the RCSB PDB has really been working hard at redesigning their resource to be more easily accessed by a wide variety of users. Below you will ........ Read more »
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 5, 2011
- 08:45 AM
- 834 views
Tip of the Week: SKIPPY predicting variants w/ splicing affects
More and more disease-causing mutations are being identified in exonic splicing regulatory sequences (ESRs). These disease effects can result from ESR mutations that cause exon skipping in functionally diverse genes. In today’s tip I’d like to introduce you to a tool designed to detect exon variants that modulate splicing. The tool is named SKIPPY and has been developed and is maintained by groups in the Genomic Functional Analysis research section of the NHGRI.
At the end of the ........ Read more »
Woolfe, A., Mullikin, J., & Elnitski, L. (2010) Genomic features defining exonic variants that modulate splicing. Genome Biology, 11(2). DOI: 10.1186/gb-2010-11-2-r20
Cline, M., & Karchin, R. (2010) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. DOI: 10.1093/bioinformatics/btq695
- October 20, 2010
- 09:09 AM
- 779 views
Tip of the Week: Comparing Microbial Databases
A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I’ve been exploring & thinking since then & am going to give a very brief comparison of those two resources in today’s tip & I’ll expand the comparison to other resources here in the text of this post.
Each of these resources could (and does in many cases) have an hour long tutorial devoted to it so I will only be able to give the briefest of ove........ Read more »
Schneider, K. (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Research, 34(90001). DOI: 10.1093/nar/gkj134
Markowitz, V., Chen, I., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Anderson, I., Lykidis, A., Mavromatis, K.... (2009) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp887
Markowitz, V., Ivanova, N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I., Grechkin, Y., Dubchak, I., Anderson, I.... (2007) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research, 36(Database). DOI: 10.1093/nar/gkm869
Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O.... (2009) The comprehensive microbial resource. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp912
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S.... (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp967
- September 27, 2010
- 08:42 AM
- 713 views
News about the Integrated Microbial Genomes (IMG) resource
I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! The........ Read more »
Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z.... (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biology, 8(8). DOI: 10.1371/journal.pbio.1000448
- September 15, 2010
- 09:05 AM
- 785 views
Tip of the Week: CircuitsDB for TF/miRNA/gene Regulation Networks
In this week’s tip I’d like to introduce you to CircuitsDB, which describes itself as:
“…a database where transcriptional and post-transcriptional (miRNA mediated) network information is fused together in order to propose and recognize non trivial regulatory combinations. “
I found out about the database from the BioMed Central article “CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse“, wh........ Read more »
Friard, O., Re, A., Taverna, D., De Bortoli, M., & Corá, D. (2010) CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics, 11(1), 435. DOI: 10.1186/1471-2105-11-435
Re, A., Corá, D., Taverna, D., & Caselle, M. (2009) Genome-wide survey of microRNA–transcription factor feed-forward regulatory circuits in human. Molecular BioSystems, 5(8), 854. DOI: 10.1039/B900177H
- September 2, 2010
- 09:32 AM
- 936 views
Briefings in Bioinformatics – our education paper is available now
Back in April I happened to mention that we (OpenHelix) were writing a paper on informal sources of bioinformatics education (in a Friday SNPets item) and we were asked to announce when the paper came out. Well, we got word late last week that the article has been published. The article appears in a special issue of Briefings in Bioinformatics that is devoted to bioinformatics education. I’m not sure if all the articles in the issue are available yet, but it looks like several are in the j........ 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. DOI: 10.1093/bib/bbq026
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