 |
|
Cloud computing brings cost of protein research down to Earth
April 10, 2009Medical College of Wisconsin's Data Analysis Cluster makes proteomics research more accessible to scientists worldwide
Researchers at the Medical College of Wisconsin Biotechnology and Bioengineering Center in Milwaukee have just made the very expensive and promising area of protein research more accessible to scientists worldwide.
They have developed a set of free tools called ViPDAC (virtual proteomics data analysis cluster), to be used in combination with Amazon's inexpensive "cloud computing" service, which provides the option to rent processing time on its powerful servers; and free open-source software from the National Institutes of Health (NIH) and the University of Manitoba.
Their research appears online in Journal of Proteomic Research and is funded by the NIH Heart Lung and Blood Institute's Proteomics Innovation Center at the Medical College. Proteomics is a biomedical research term used to describe the large-scale study of all the proteins expressed by an organism. It usually involves the identification of proteins and determination of their modifications in both normal and disease states.
One of the major challenges for many laboratories setting up proteomics programs has been obtaining and maintaining the very costly computational infrastructure required for analysis of the vast flow of proteomics data generated by mass spectrometry instruments used to determine the elemental composition as well as chemical structure of a molecule, according to senior investigator, Simon Twigger, Ph.D., assistant professor of physiology.
"We're applying this technology in our Proteomics Center to study cardiovascular disease, the effects of radiation damage, and in our collaboration with the University of Wisconsin- Madison stem cell research group," he says.
With cloud computing making the analysis less expensive and more accessible, many more users can set up and customize their own systems. Investigators can analyze their data in greater depth than previously possible, making it possible for them to learn more about the systems they are studying.
"The tools we have produced allow anyone with a credit card, anywhere in the world, to analyze proteomics data in the cloud and reap the benefits of having significant computing resources to speed up their data analysis," says lead author Brian Halligan, Ph.D., research scientist in the Biotechnology and Bioengineering Center.
"For researchers currently without access to large computer resources, this greatly increases the options to analyze their data. They can now undertake more complex analyses or try different approaches that were simply not feasible for them before."
Until recently, the standard software programs used for proteomics data analysis were almost exclusively commercial, proprietary and expensive. Fees for commercial applications typically rivaled or exceeded the cost of the hardware to run them.
In 2004, a group from the NIH developed and distributed an open-source alternative to commercial proteomics search programs, entitled Open Mass Spectrometry Algorithm (OMSSA). A second open-source proteomics database search is also now available; the X!Tandem, developed and released by the Bevis Laboratory at the University of Manitoba.
A link on the College's Proteomics Center website http://proteomics.mcw.edu/vipdac provides detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters, as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases.
"We describe a system that combines distributed-on-demand cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without a huge investment in computational hardware or software licensing fees," says Dr. Halligan.
"The pricing structure of distributed computing providers such as Amazon Web Services allows laboratories, or even individuals, to have large-scale computational resources at their disposal at very low cost per run."
Medical College of Wisconsin
Their research appears online in Journal of Proteomic Research and is funded by the NIH Heart Lung and Blood Institute's Proteomics Innovation Center at the Medical College. Proteomics is a biomedical research term used to describe the large-scale study of all the proteins expressed by an organism. It usually involves the identification of proteins and determination of their modifications in both normal and disease states.
One of the major challenges for many laboratories setting up proteomics programs has been obtaining and maintaining the very costly computational infrastructure required for analysis of the vast flow of proteomics data generated by mass spectrometry instruments used to determine the elemental composition as well as chemical structure of a molecule, according to senior investigator, Simon Twigger, Ph.D., assistant professor of physiology.
"We're applying this technology in our Proteomics Center to study cardiovascular disease, the effects of radiation damage, and in our collaboration with the University of Wisconsin- Madison stem cell research group," he says.
With cloud computing making the analysis less expensive and more accessible, many more users can set up and customize their own systems. Investigators can analyze their data in greater depth than previously possible, making it possible for them to learn more about the systems they are studying.
"The tools we have produced allow anyone with a credit card, anywhere in the world, to analyze proteomics data in the cloud and reap the benefits of having significant computing resources to speed up their data analysis," says lead author Brian Halligan, Ph.D., research scientist in the Biotechnology and Bioengineering Center.
"For researchers currently without access to large computer resources, this greatly increases the options to analyze their data. They can now undertake more complex analyses or try different approaches that were simply not feasible for them before."
Until recently, the standard software programs used for proteomics data analysis were almost exclusively commercial, proprietary and expensive. Fees for commercial applications typically rivaled or exceeded the cost of the hardware to run them.
In 2004, a group from the NIH developed and distributed an open-source alternative to commercial proteomics search programs, entitled Open Mass Spectrometry Algorithm (OMSSA). A second open-source proteomics database search is also now available; the X!Tandem, developed and released by the Bevis Laboratory at the University of Manitoba.
A link on the College's Proteomics Center website http://proteomics.mcw.edu/vipdac provides detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters, as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases.
"We describe a system that combines distributed-on-demand cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without a huge investment in computational hardware or software licensing fees," says Dr. Halligan.
"The pricing structure of distributed computing providers such as Amazon Web Services allows laboratories, or even individuals, to have large-scale computational resources at their disposal at very low cost per run."
Medical College of Wisconsin
Proteomics Current Events and Proteomics News RSSProtein changes in heart strengthen link between Alzheimer's disease and chronic heart failure
A team of U.S., Canadian and Italian scientists led by researchers at Johns Hopkins report evidence from studies in animals and humans supporting a link between Alzheimer's disease and chronic heart failure, two of the 10 leading causes of death in the United States.
Will genomics help prevent the next pandemic?
This week, the Public Library of Science, an open-access publisher, presents the "Genomics of Emerging Infectious Disease," a collection of essays, perspectives, and reviews that explores how genomics-with all its associated tools and techniques-can provide insights into our understanding of emerging infectious disease.
How Proteins Talk to Each Other
Investigators at Burnham Institute for Medical Research (Burnham) have identified novel cleavage sites for the enzyme caspase-3 (an enzyme that proteolytically cleaves target proteins).
Drug discovery process more accurate, less expensive using novel mass spectrometry application
Cancer and cell biology experts at the University of Cincinnati (UC) have developed a new mass spectrometry-based tool they say provides more precise, cost-effective data collection for drug discovery efforts.
Weill Cornell Researchers Discover New Anti-Tuberculosis (TB) Compounds
Attempts to eradicate tuberculosis (TB) are stymied by the fact that the disease-causing bacteria have a sophisticated mechanism for surviving dormant in infected cells.
Scientists Use MicroRNAs to Track Evolutionary History for First Time
The large group of segmented worms known as annelids, which includes earthworms, leeches and bristle worms, evolved millions of years ago and can be found in every corner of the world.
Conaway Lab uncovers function of potential cancer-causing gene product
The Stowers Institute's Conaway Lab has uncovered a previously unknown function of a gene product called Amplified in Liver Cancer 1 (Alc1), which may play a role in the onset of cancer.
What makes stem cells tick?
Investigators at the Burnham Institute for Medical Research (Burnham) and The Scripps Research Institute (TSRI) have made the first comparative, large-scale phosphoproteomic analysis of human embryonic stem cells (hESCs) and their differentiated derivatives.
New Tool May Help with Early Detection of Deadly Pancreatic Cancer
A new diagnostic tool developed by Van Andel Research Institute (VARI) scientists has shown promising results when used with patients of pancreatic cancer, one of the deadliest forms of cancer due to the difficulty of diagnosing it in its early stages.
Preimplantation genetic diagnosis may pose neurological risks
Preimplantation genetic diagnosis (PGD) has helped many couples conceive healthy children and is generally considered a safe practice.
More Proteomics Current Events and Proteomics News Articles
 |
Principles of Proteomics (Advanced Text Series) by R. M. Twyman (Author) The Advanced Text series is designed for students taking advanced-level courses, including upper-level undergraduates and graduate students. Titles in this series will also be invaluable to researchers new to a field, and to established researchers as a basic reference text. Proteomics is a major new area of scientific research driven by the growing information gap between genes and their functions. Large-scale DNA sequencing and annotation projects identify thousands of new genes on a daily basis but the functions of these genes remain largely unknown. Proteins are the actual functional molecules of the cell, and technical advances in the high-throughout analysis of proteins now allow these molecules to be studied directly. Principles of Proteomics provides a comprehensive... |
 |
Proteomics in Practice: A Guide to Successful Experimental Design by Reiner Westermeier (Author), Tom Naven (Author), Hans-Rudolf Höpker (Author) A combined review, manual and reference for the successful analysis of proteins using the classical approach of 2-D gel electrophoresis, mass spectrometry and related sequence database inquiries. The first section, written in a textbook style, introduces the entire technology, while the second section represents a comprehensive laboratory manual spanning the full range of methods from sample preparation to protein identification. Alternative methods and procedures are only suggested for those cases where the "default" procedure would fail to deliver adequate results. The third section is a unique troubleshooting guide, designed to answer many of the frequently asked questions regarding proteome analysis. The final section contains a thorough reference list to guide interested... |
 |
Proteomics: A Cold Spring Harbor Laboratory Course Manual by Andrew J. Link (Author), Philip Andrews (Author), Joshua LaBaer (Author) Based on a popular course at Cold Spring Harbor Laboratory, this new manual assembles cutting-–edge protocols, helpful hints, and lecture notes to teach researchers from a wide variety of disciplines the essential methods of proteomics using state-–of-–the-–art instrumentation. Detailed protocols involving protein microarrays, liquid chromatography, high-–throughput cloning of expression constructs, IMAC, mass spectrometry, MALDI-–TOF, and MudPIT are provided, along with well-–illustrated descriptions of experimental procedures and lists of recommended Web sites and reading material. Proteomics: A Cold Spring Harbor Laboratory Course Manual can be used both as the basis for a course and as a detailed bench manual for those performing indispensable proteomic... |
 |
Introduction to Proteomics (Wiley - Interscience Series on Mass Spectrometry) by Agnieszka Kraj (Editor), Jerzy Silberring (Editor) Introduction to Proteomics is written by seasoned researchers with years of practical experience. In addition to comprehensive discussions of the basic concepts, techniques, and applications of the subject, the text also includes an extensive glossary and a chapter containing laboratory exercises and protocols. While mass spectrometry is central to proteomics, the book discusses all of the analytical techniques a student is likely to need when faced with real-world problems, such as sample preparation, chromatographic and electrophoretic separation, micro-total analysis systems, and bioinformatics. |
|
Anticancer Research C-W Cancergenomics & Proteomics C-W in V by Iiar % Dr John G Delinassios | |
|
Biofilm Biotechnology: Recent Advances in the Understanding of Proteomics, Genomics, and Signaling in Biofilms CD-ROM Starring: Bill Costerton Directed By: Ryan Jordan | |
 |
Introduction to Proteomics: Tools for the New Biology by Daniel C. Liebler (Author) Univ. of Arizona, Tucson. Pocket-sized introduction to new proteomic technologies and data mining tools. Includes generic examples illustrating important proteomics applications and compares the advantages and disadvantages of different proteomic tools and approaches. Hardcover, softcover also available. |
|
Bioinformatics, Genomics, and Proteomics: Getting the Big Picture, DVD, Biotechnology in the 21st Century by Films for the Humanities & Sciences If the 20th century was the era of physics and nuclear fission, the 21st belongs to the life sciences. Moving from gene, to genome, to genetically based diseases, this program provides an overview of the interrelated fields of genomics, proteomics, and bioinformatics, with an emphasis on practical applications of biotechnology to the field of medicine. Are genetically personalized drugs around the next corner? Commentary is provided by Bob Forgey, of ProNAi Therapeutics; Bill Worzel and Jeanne Orhnberger, of Genetics Squared; and Drs. Brian Athey and Elliott Hill, of the University of Michigan. A Films for the Humanities & Sciences Production. (25 minutes) 2009 DVD, Retail $99.95 | |
 |
Proteomics Sample Preparation by Jörg von Hagen (Editor) This long-awaited first guide to sample preparation for proteomics studies overcomes a major bottleneck in this fast growing technique within the molecular life sciences. By addressing the topic from three different angles -- sample, method and aim of the study -- this practical reference has something for every proteomics researcher. Following an introduction to the field, the book looks at sample preparation for specific techniques and applications and finishes with a section on the preparation of sample types. For each method described, a summary of the pros and cons is given, as well as step-by-step protocols adaptable to any specific proteome analysis task. |
 |
Discovering Genomics, Proteomics and Bioinformatics (2nd Edition) by A. Malcolm Campbell (Author), Laurie J. Heyer (Author) KEY BENEFIT: Discovering Genomics is the first genomics text that combines web activities and case studies with a problem-solving approach to teach upper-level undergraduates and first-year graduate students the fundamentals of genomic analysis. More of a workbook than a traditional text, Discovering Genomics, Second Edition allows students to work with real genomic data in solving problems and provides the user with an active learning experience. KEY TOPICS: Genomic Medicine Case Study: What’s wrong with my child? Genome Sequence Acquisition and Analysis, Comparative Genomics in Evolution and Medicine, Genome Variations, Genomic Medicine Case Study: Why Can’t I Just Take a Pill to Lose Weight? Basic Research with DNA Microarrays,... |
| © 2009 BrightSurf.com |