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November 11, 2009
Feature - Big science facilities meet the cloud

Feature - Big science facilities meet the cloud

Dylan Maxwell explains the Science Studio system to a bystander at Summit 2009 in Banff, Alberta. Photo by Miriam Boon.

Lab notebooks are so passé. In the brave new world of cloud computing, the entire experimental process will take place in your web browser.
And if a team of Canadian researchers at the University of Western Ontario and the Canadian Light Source in Saskatchewan has anything to say about it, researchers around the world will be using a web platform called Science Studio.
“One of the aims of Science Studio is to be able to access big science facilities such as the Canadian Light Source,” said Marina Fuller, a chemistry researcher with the project. “It’s a complete experiment management system.”
The test case for Science Studio is the VESPERS beamline at the Canadian Light Source synchrotron. When Science Studio is complete in 2011, researchers will be able to use the platform to apply

November 4, 2009
News of the Week - Update from Asia

Feature - Vietnam welcomes three new grid sites; hospitals get new ‘HOPE’

Participants from ACGRID school at Institute for Francophone Informatics (IFI) in Hanoi, October 2009. Image courtesy ACGRID. Image of Vietnamese flag on front page courtesy Wikipedia/Creative Commons

Vietnam hosts some of the world’s most biodiverse areas — with six biosphere reserves — along with one of the lowest unemployment rates in the third world and, as of last month, three of the newest grid sites to join the world’s largest grid computing infrastructure.EUAsiaGrid was launched in April of 2008 to foster grid computing technology within Asia, and to create ties between the e-Infrastructure communities of Asia and Europe. Last month, EUAsiaGrid partners co-organized with the French research institute Centre National de la Recherche Scientifique (CNRS) the second ACGRID school, or Advanced Computing and Grid Technologies for Research, to train current and up

September 9, 2009
Feature - A SLiM chance for viruses

Feature - A SLiM chance for viruses

Viruses hijack the replication machinery of cells. Image courtesy Simon Hettrick

Viruses have evolved a clever way of reproducing. They hijack the replication machinery of their host cell, which is controlled and regulated by a variety of signaling pathways, and fool them into producing copies of the virus.
Richard Edwards, head of the Bioinformatics and Molecular Evolution group at the University of Southampton, UK, is trying to better understand signaling pathways in order to develop treatments for viruses — and for diseases that operate similarly.  This is an enormous task, because to understand signaling pathways in the human body requires studying the interactions between the 20,000 or so proteins contained within the cells.
To do so, Edwards is focusing on short, linear motifs known as SLiMs. “A protein can be thought of as a sequence of amino acids, like beads on a string” explains Edwards. “[SLiMs] consist o

August 26, 2009
Feature - Asian computers join forces against avian flu

Feature - Asian computers join forces against avian flu

Computer simulation of potential drug candidate attacking avian flu virus. Image courtesy Dr. Ying-Ta Wu, Academia Sinica, Taiwan 

Dealing with deadly diseases is not just a matter of test-tubes and petri dishes. Increasingly, grid computing is being used to simulate the ways that new drugs could attack viruses, looking for a magic bullet that could cure diseases or even prevent epidemics.
Computers can simulate a large number of chemical compounds and measure their ability to fit snugly into the chemical coating of a virus, thereby blocking its ability to function properly. Launched in March 2009, this so-called “Avian Flu DC2 Refinement” is the latest attack on avian flu using grid computing power. This initiative is supported by the EUAsiaGrid community, a partnership of Asian and European research institutions co-funded by the European commission to foster new uses of grid computing for science and society

August 26, 2009
Feature - Improving Alzheimer's research a million scans at a time

Feature - Improving Alzheimer’s research, a million scans at a time

Alzheimer’s is one of the most feared diseases associated with aging. Fortunately, early detection can slow its development. Image courtesy stock.xchng

As you read this, your brain is busily working. In a complex but unconscious process, it scans the pixels on your screen, analyzes the images and turns them into meaningful information.
This week, a similar work began, neuGRID, that might help keep our minds whirring wonderfully as we (alas) age.
This massive scanning project will feed 6,300 magnetic resonance (MR) scans from more than 700 patients — a bit less than 200 images per patient, making for an impressive total of 1,260,000 images — through an automated series of calculations. This “pipeline” will analyze the cortical thickness of the brain (a measurement aligned with brain health) and its deterioration over time. The images are from the Alzheimer’s Disease Neur

August 12, 2009
Video - Health-E Child video documentary

 

Video of the Week: Health-e-Child documentary

Athenaweb, one of the hosts for the Health-e-Child video, can be thought of as “the YouTube of science,” with hundreds of films and videos available. Image courtesy Athenaweb 

The Health-e-Child project (See iSGTW 28 May, 2008 and the 8 July, 2009 HealthGrid roundup) has video documentaries about its work that can now be seen as broadcasts on the Euronews website. (Click on the “Science-Tech” banner up on the right.) The first broadcast is entitled “New frontiers of imaging the human body.”
All European public televisions and main private ones receive the broadcasts, and some of them will be re-aired during the summer. 
They are also accesible on YouTube and other smaller, regional streaming online websites. The reports will be also broadcast on athenaweb.org, a website specializing in Worldwide Research TV reports.
A special broadcast has also been scheduled for Friday, September

July 8, 2009
News of the Week - HealthGrid roundup

News of the Week - HealthGrid roundup

Brandenburg Gate. Image courtesy stock.xchng 

 

Last week, Berlin hosted the 7th HealthGrid conference, from 29 June – 1 July. The feeling pervading the event was that the HealthGrid community had progressed a long way — and yet for grids to reach their full promise in the area of health care, a lot of work remains.“I first participated in the conference three years ago in 2006,” said Xin Zhou, a conference presenter and maintainer of the grid infrastructure inside the University of Geneva Hospital. He added, “Back then, we were talking about ‘the plan.’ Many people then presented what they were going to do; now they are presenting the applications. This represents real progress in the research domain and shows movement towards practice.”Simple intuitive interfaces, appealing to non-specialist users, were an oft-called for commodity. In a demonstration of just such an interface, Tobi

July 1, 2009
Feature - Cancer knowledge cloud for a new generation of medicine

Feature - Cancer Knowledge Cloud for a new generation of medicine

Kenneth Buetow, shown speaking at a conference in 2005.Image courtesy of NCRI.

Kenneth Buetow is the National Cancer Institute’s Associate Director of Bioinformatics and IT, and Director of the Center for Biomedical Informatics and IT, where he initiated and oversees the caBIG (cancer Biomedical Informatics Grid) program. He spoke last April at the Bio-IT World conference on caBIG: An interoperable IT framework for uniting research and care.
Thinking BIGKen Buetow thinks BIG.  He envisions what he calls a Cancer Knowledge Cloud — an IT environment designed to foster information connectivity among cancer patients, cancer researchers and clinical care providers. This environment, powered by caBIG tools and infrastructure, would enable a continuous and accelerated cycle of discovery, diagnostic and pharmaceutical product development, and improved clinical care.Cancer care and research still operate on a lin

June 17, 2009
Feature - Grid-enabled virus hunting

Feature - Grid-enabled virus hunting

3D replica of senecavirus, a pathogen discovered several years ago by researchers in Pennsylvania. UC San Francisco researcher Eric Delwart and his colleague Chunlin Wang of Stanford University use the RENCI-developed TeraGrid Science Gateway and the Open Science Grid to access grid computing resources in their search for new viruses.
Image courtesy of the Institute for Animal Health, UK

Researchers use distributed computing to make sequence analysis faster and easier.DNA sequencing and sequence analysis happens daily in many biological sciences laboratories, but analyzing large sets of genetic data increasingly requires computing resources beyond the capabilities of most labs. The search for the best hardware and software led Eric Delwart, a professor of laboratory medicine at the University of California, San Francisco, and a senior investigator at the Blood Systems Research Institute, and Chunlin Wang, a research associate at the Stanford Univ

June 17, 2009
Feature - Swine flu and the grid: A researcher's view

Feature - Swine flu and the grid: A researcher’s view As the name suggests, “Swine Flu” may have its origins among pigs, and then may have made the jump across species to humans. Image courtesy Janne Brodin, stock.exchng (Editor's note: Swine Flu — or H1N1 influenza A — has been in the headlines lately. The World Health Organization has officially classified the latest outbreak a “pandemic,” in response to its world-wide geographic spread. To find out more about how the grid fits in with research to fight this virus, we asked Ana Lucia Da Costa of HealthGrid, who formerly worked at CNRS France, to give her viewpoint from the lab.) The emergence of a new influenza epidemic such as this is an opportunity for the grid to contribute to international public health response. It has highlighted the importance of providing the right information to decision-makers as quickly as possible. Grid technology is particularly well fitted to

June 3, 2009
Feature - Clarity in clinical care

Feature - Clarity in clinial care: achieving fully interoperable databases

Werner CeustersImage courtesy of W. Ceusters.

Werner Ceusters, director of the  Ontology Research Group at the NYS Center of Excellence in Bioinformatics & Life Sciences, spoke at the Bio-IT World Conference in Boston this past April on the topic of "Do Healthcare IT Standards Hamper the Advance of Science?" 

“Swimming is healthy and contains eight letters.” Absurd? Of course — the real thing is confused with its symbolic representation. Absurdity, then, abounds in current Electronic Health Records (EHRs) according to Werner Ceusters of the New York State Center of Excellence in Bioinformatics and Life Sciences and the University at Buffalo. A polyp by any other name… A significant and universal problem with legacy EHRs, Ceusters says, is that software programs that access them cannot adequately differentiate between diagnoses for a given patient and link them prope

June 3, 2009
Image of the week - Melanoma image analysis

Image of the week - Melanoma image analysis

Nancy Thomas, an associate professor in the School of Medicine at the University of North Carolina specializing in melanoma research, leads the Melanoma Image Analysis project. Her team is looking at the use of image analysis approaches to aid in diagnosis and prognosis of melanoma from patient pathology slides. Based on prior research from Thomas and others, we know that observable characteristics of melanoma can stem from more than one type of genetic mutation.This project is working under the hypothesis that image analysis will allow for the quantitative extraction of melanoma features and that such features can be used to both identify cancerous tissues and link melanoma phenotype with genotype. If true, this will lead to enhanced prediction of patient survival and guide future treatment options. The research should result in a more robust and clinically relevant melanoma classification system based on causal pathways.Computing experts at the Re

May 20, 2009
Announcement - 2009 caBIG Annual Meeting, Washington, D.C.

Announcement - 2009 caBIG® Annual Meeting, Washington, D.C.

Image courtesy of cabig.nci.nih.gov

Event: caBIG® 2009: Solving basic and clinical research challenges in cancer and beyond
Venue: Marriott Wardman Park Hotel, Washington, D.C., U.S.
Dates:

Meeting: 20-22 July 2009 Deadline for booking hotel rooms at discounted rate: 19 JuneAbstract submissions due: 29 May

Meeting Web site
Registration 
Preliminary program

Attendees will hear how caBIG® is accelerating biomedical research through interoperable tools, infrastructure, standards, and policies that enable data-sharing and collaborations that transcend institutional, geographical, and disciplinary boundaries. The meeting will feature:

Case studies and best practices in clinical trials management, in vivo imaging, molecular analysis, tissue banking and pathology, and data-sharing and security
Tips on implementing, adapting, and customizing caBIG® tools and infrastructure
Presentations o

May 13, 2009
Feature - EDGeS helps us all talk to each other

Feature - EDGeS helps us all talk to each other

With AutoDock, biologists can predict how small molecules will interact with known larger molecules - vital to evaluating candidates for new drugs. Image courtesy www.YASARA.org

Like Bill Murray adrift in Japan in the movie “Lost in Translation,” things can go awry when service grids and volunteer grids try to talk to each other.
Service grids, such as EGEE, often involve large institutions whose work method is centered around collaboration — to the point where participants often know each other personally. To ensure security, resources and users pass through an accreditation process, and the resulting “certificate” provides proof that this occurred successfully. The certificate is key to allowing jobs to be submitted and completed.
On the other hand, volunteer systems — such as BOINC or XtremWeb-based desktop grids — consist of large numbers of personal computers linked together by individuals w

March 11, 2009
iSGTW Feature - Be still, my heart

Feature - Be still, my heart A  whole ventricular model showing reentrant activity in the ventricles. The arrows show the direction of wave propagation. Image courtesy Thushka Maharaj It’s a familiar scene on television shows such as “ER”: A patient’s heart is beating improperly, a doctor puts a pair of electrical paddles against her chest, yells “clear,” gives an electric shock — and whew, the heart starts beating again normally. The whole process, known as “defibrillation,” is relatively common in real-life emergency rooms. But what is really happening, and why does it work? Thushka Maharaj, a doctoral student within the Computational Biology Group at the University of Oxford, hopes to answer these questions. She is part of an international collaboration studying the effects of applying electrical shocks to both healthy and diseased hearts to understand exactly how defibrillation works. In order to do so, she simulates on computers the application of electric shocks

February 4, 2009
iSGTW Image of the Week - ThIS cancer therapy

  Image of the week - ThIS cancer therapy  ThIS is an acronym for Therapeutic Irradiation Simulator for cancer therapy, which simulates the irradiation of a patient with carbon ion beams in order to allow clinicians to compute the 3D dose distributions inside the patient for a computer-aided tomography (CT) scan.Such simulations are very computing intensive, requiring thousands of hours on a single CPU. But by putting ThIS on the EGEE Grid, one simulation can be split into independent sub-simulations executed concurrently on different CPUs, speeding up the job.The project is now being integrated into the OpenGATE project. The developers — Sorina Camarasu, Tristan Glatard, Laurent Guigues, Thibault Frisson and David Sarrut, of CNRS in Lyon, France — say “The results are promising and we are confident that this advanced submission method will help the simulator to reach a larger research and medical community. Moreover, since most users need a higher-level graphical user in

February 4, 2009
iSGTW Opinion - Grids for optimizing cancer radiotherapy

Opinion - Grids for optimizing cancer radiotherapy treatment (The author, Dimitri Dimitroyannis, is a board-certified, clinical medical physicist at Kansas City Cancer Centers, who trained in experimental high-energy physics. This summary is rewritten from his longer article in Medical Physics Web.) Transverse slice from an actual computer-aided tomography image of a patient with cancer at the base of the tongue. Soft tissue appears as light grey, while bone is whitish. Red area is the cancerous target that needs to be irradiated. The three yellow areas correspond to uninvolved tissues that need to receive as little radiation as possible — the spinal cord (center) and the two parotid glands (left and right). Image courtesy of Dimitri DimitroyannisAbout 4 million European and North American citizens will be diagnosed with cancer this year. More than half of these new cancer patients will receive radiotherapy for the treatment of their disease, along with surgery and chemotherapy as appropriate. However, treating cancer patient

January 14, 2009
iSGTW Announcement - CCGrid Health Workshop, Shanghai, May 2009

Announcement - CCGrid-Health Workshop, Shanghai, May 2009 Image courtesy of www.healthcarecomputing.com  Challenges for the application of Grids in Healthcare This workshop is organized in conjunction with the CCGrid conference, in Shanghai, China, 18-21 May 2009.The workshop will provide application developers and computer scientists the opportunity to share and discuss on-going efforts in health-related grid applications and the associated technologies, achievements, gaps, and roadblocks; and to disseminate healthgrid requirements in the grid research community.Important datesPAST Papers Due: 30 December 2008Notification of Acceptance: 30 January 2009Camera-Ready Papers: 15 February 2009Workshop: May 2009OrganizationTony Solomonides University of West EnglandBristol, United KingdomTristan Glatard CREATIS, CNRS, Lyon, FRSilvia D. Olabarriaga Academic Medical Center, University of Amsterdam, NL  

December 3, 2008
iSGTW Award of the week: Health-e-Child wins best exhibit at ICT 2008

Award of the week - Health-e-Child wins Exhibit Grand Prize at ICT 2008 From left: Jerôme Revillard, David Manset, both of MAAT Gknolwedge, and Antii Peltomäki, Deputy director of DG-INFSO at the European Commission. Image courtesy of ICT 2008 Health-e-Child has won the ICT 2008 Exhibit Grand Prize worth €10,000. ICT is the largest European conference of the year on Information and Communication Technologies, and was held in Lyon, France last week, 25-27 November.Health-e-Child is a European distributed computing project that fits grid technology to pediatric medicine. It connects hospitals and participating institutions—allowing them to share integrated, multi-level information. Runners up to Health-e-Child at ICT 2008 include HoloVizio in second place and u-2010 in third. Congratulations to all the winners! Read more.iSGTW reported on Health-e-Child in May 2007, Health-e-Child prepares for deployment, and again this past May, Health-e-Child: one year on.   

December 3, 2008
iSGTW Feature - Protein structure: taking it to the bank

Feature - Protein structure: taking it to the bank At left, the predicted (gold) and experimental (blue) structure of 30S ribosomal protein S27A from Thermoplasma acidophilum.At right, the same for protein G. Xu′s team participated in the 2008 Critical Assessment of Structure Prediction (CASP) competition, sponsored by NIH, BioSapiens Network and the European Molecular Biology Organization, in which participants are given 120 proteins with unknown structures to predict. RAPTOR ranked among the top 5 of 85 teams.  Thermoplasma acidophilum, represented above, was a test protein used in CASP.Image courtesy of Jinbo Xu. Properly functioning proteins are essential for our bodies. A protein’s structure, the folded form its amino acid string assumes, determines its function.  Scientists know the sequence and structure of about 50,000 proteins—out of millions. They keep this valuable information in a “bank”—the NSF- and NIH-funded Protein Data Bank.  To predict the structure of a newly ide

November 5, 2008
iSGTW Feature - Alzheimers-Parkinsons interaction

Feature - UCSD investigates Alzheimer’s–Parkinson’s interaction Representation of the cell membrane (green) in "ball-and-stick" form where the balls represent the centers of atoms and the sticks represent the covalent bonds between them.  (See other figure caption for color legend.) The Abeta (orange) is shown in water-accessible form. Image courtesy of Igor Tsigelny. In patients with both Alzheimer’s and Parkinson’s, the Parkinson’s disease can progress at an accelerated rate due to an abnormal protein interaction. A team of University of California San Diego (UCSD) researchers is studying this interaction, contributing to the search for a drug that will slow this devastating progression.Alpha-synuclein (aS) is a protein that accumulates on neural cells in patients with Parkinson’s disease. Through modeling simulations run on San Diego Supercomputing Center (SDSC) resources, the researchers have found that aS can interact abnormally with Abeta amyloid—the protein tha

October 15, 2008
iSGTW Feature - Volunteer computing helps track malaria

Feature - Volunteer computing helps track malaria Thousands of volunteers are contributing to the project from all over the globe. Image courtesy of Nicolas Maire How do you predict the results of a malaria vaccine? With the grid, and volunteer computing.A research team at the Swiss Tropical Institute, or STI, in Basel studied the use of computer simulations to predict the epidemiological impact of potential malaria vaccines.  These predictions were obtained with the help of thousands of volunteers who made their computers available to Malariacontol.net, a volunteer computing project based on the Berkeley Open Infrastructure for Network Computing (BOINC).Malaria is one of the world’s leading public health problems, estimated to cause over a million deaths per year. Mathematical modeling of malaria, such as that done on computer, can help public health experts predict the epidemiological impact and cost effectiveness of vaccines and other malaria control interventions.Because running such simulation models is computatio

September 17, 2008
iSGTW Feature - Preventing human-transmissible avian flu

Feature -  Grid helps to clip the wings on avian flu The simulated tetramer neuraminidase (N1) system is shown encased in a water bath.  (Pink, purple, red and green objects are all N1; represented in "skeleton" and "skin" images, respectively. The colors are not significant.) One chain is shown with a green molecular surface (skin) representation. Oseltamivir (also known as Tamiflu, the only effective drug available orally) is shown bound in yellow within each of the active sites of the (green) N1 enzyme. Oseltamivir is represented as blue, red and white ball-and-sticks in the other portions.Image courtesy of NBCR. To date the avian flu virus is not transmissible among humans, however it mutates constantly and some strains have already become resistant to current anti-viral drugs. With the possibility of a worldwide outbreak ever-present, the search for new, more powerful drugs is vital.Using resources at the San Diego Supercomputing Center (SDSC), a team of University of California San Diego scienti

July 30, 2008
iSGTW Feature - The future of public health: grid gains traction

Feature - The future of public health: The grid gains traction Dr. Ida A. Bengston (1881-1952) was one of the first women employed on the scientific staff of the Hygienic Laboratory of the Public Health Service, the predecessor to the National Institutes of Health. Bengston was particularly noted for her studies of bacterial toxins.This photo is symbolic of the importance of laboratory equipment to the CDC’s progress in the improvement of world wide public health standards.Image courtesy of CDC, Betty Partin. Drawing on data located in Washington, Oregon and Idaho, a University of Washington researcher simulates a tuberculosis outbreak in these three states and shares her work with researchers throughout the country. Well, not so fast—seamlessly gathering and distributing information in this way is still a vision of the future being brought to life by Tom Savel and his colleagues at the National Center for Public Health Informatics (NCPHI), part of the Centers for Disease Control and Prevention (CDC).The U.S. public h

July 30, 2008
iSGTW Link of the week - Life sciences database

Link of the week - Life sciences database Image courtesy of lsdb.bii.a-star.edu.sg  Directory service systemThe Life Science Database Directory aims to be a one-stop directory service for Life Science related databases. This effort is coordinated by the Life Sciences Virtual Grid Community (chaired by Dr. Patrick Tan, NCC) under the umbrella of Singapore's National Grid, with contributions from many organizations.Find:Life sciences mirrored databases Post publication databases  Read more.