Welcome to the International Symposium on Grids and Clouds 2012

This week the GridCast team is in Taipei, reporting from the International Symposium on Grids and Clouds 2012. Already it feels like much less than a year since the last time we were in Taipei, and we are busy catching up with our friends and colleagues here at Academia Sinica and from across the region.

2012 is the 10 year anniversary of ISGC, and over the last decade it has followed how individual, innovative researchers across the Asia Pacific region have converged into a coherent community, sharing their knowledge and experiences along the way.

GridCast will be blogging from the event, alongside other delegates to bring you behind-the-scenes reports. We are also very pleased that our new Asia Pacific iSGTW Editor, Vivian Tiän-Tiän Chang will be reporting from ISGC. Vivian is based at the Academia Sinica Grid Computing Centre, and you can read about how she will be reporting from the region in iSGTW. Welcome to the team Vivian!

An ISGC 2010 Reflection

This is Andy Turner's last in a series of GridCast posts about ISGC 2010. His previous post is here. A list of all his posts in chronological order is as follows:
* An ISGC 2010 GridCast Introduction
* A First Full Day Back
* Day of the Social Simulation Tutorial
* Day of the iRODS Workshop
* From Infrastructure towards Applications Research
* A Walk in the Sunshine
* An ISGC 2010 Reflection

I am writing this after a short break following my return from Taiwan to the UK. Bob Jones has already posted his ISGC 2010: Round up, so this is just a brief personal reflection on the event from me, more details of what I got up to can be found here. All GridCast posts tagged with "ISGC 2010" should be available here.

To start with I'd like to add my thanks to the organisers and local hosts. ISGC 2010 was a well organised event and the local hosting was exceptional (food, entertainment, accommodation and information).

ISGC events focus on computational infrastructure and providing resources for science and society on both an international and local level. Learning about what resources exist and how they can be accessed is key for an applications focussed researcher like myself, but details of infrastructure management and provision is not very interesting. However, having an ear out during more infrastructure focussed sessions whilst doing other things was worthwhile. One thing I enjoyed in learning about the infrastructure work was the appreciation of the importance of people to the organisations delivering it. For instance in the Grid Security and Networking I Session, Mingchao Ma talking about Grid Operational Security in the UK reflected on the need for a trusted and stable team of people "that know each other".

The importance of people in organisations theme took centre stage in the brilliant key note "A contribution to e-Wissenschaft" by Tobias Blanke where the focus was on people connections and the applied use of infrastructure for humanities research. A focus "connecting people" summarises the event in my view, the coming together of a cross section of the eResearch community is important for our work, and the coming together of people from different places helps us develop an appreciation of each others cultures and concerns so we can live together in peace and harmony.

What I liked most about this event was meeting people and making friends, it is what I look forward to about most events, but at ISGC 2010, like ISGC 2009, the people were friendly and it was a pleasure. In terms of work, this has helped develop some existing collaborations and formed the basis for new ones, friendship and trust.

One further thing to note that pleased me (as a geographer) was the considerable number of specifically geographical applications presented in the sessions. We are all geographers to some extent!

Farewell, and long live GridCast, maybe I will post more for you another time :-)

ISGC 2010: Round up

(Posted on behalf of Bob Jones, Enabling Grids for E-sciencE project director)

The week-long ISGC2010 came to an end on Friday 12 March. It  focussed on data driven e-Science highlighting use cases and successful applications of distributed computing infrastructures in the Asia Pacific region. There was a mixture of plenary and parallel sessions as well as a poster exhibition. A series of workshops and tutorials preceded the symposium, attracting 70 people.

The symposium attracted more than 150 participants from 27 countries spanning Asia, Europe and the Americas. The keynotes by invited speakers highlighted the impact of distributed computing infrastructures in research disciplines such as social sciences and humanities, civil protection, paediatrics and high energy physics. Having identified important use cases, further keynotes outlined plans for their long-term support and the move towards sustainable infrastructures across Asia, Europe and Latin America. Plenary sessions entitled Grid Activities in Asia Pacific surveyed the state of grid deployment across 12 Asian countries.
For the first time there was participation from Latin American colleagues which opened possibilities for cooperation between groups in Asia and Latin America the two regions on research in the domain of natural disaster mitigation, epidemic studies and drug discovery for diseases such as dengue fever and malaria.

Through the parallel sessions, the impact of distributed computing infrastructures in disciplines such as social sciences and humanities, life sciences, earth sciences, high energy physics, digital libraries and natural disaster mitigation. Operational procedures, middleware and security aspects were addressed in a dedicated sessions. A subject which has seen a growing interest is the integration of grid and clouds with a very popular series of talks to the point that we are considering renaming ISGC the International Symposium on Grids and Clouds.

A number of projects, many co-funded by the European Commission, are coming to close during the first half of 2010, so the symposium provided the occasion for them to present their results and lessons learnt. At the same time a number of new projects are starting and hence can build on the result and experiences of their predecessors. A key subject that was in the minds of participants from all regions was how to ensure the long-term availability of distributed computing infrastructures for the research communities. A clear value of the symposium was that participants from different continents could compare their experiences, identifying common questions and barriers to sustainability and profiting from each other experiences to develop solutions.

For the first time, the symposium was covered online in real-time by the GridCast team from the GridTalk project. A running blog including summarises of specific sessions as well as video interviews with keynote speakers and personalities and photos

Prof. Simon Lin organised an intense social programme with a gastronomic tour of Taipei culminating with a banquet for all the symposium’s participants at the Howard Plaza hotel.

I would like to thank all the members of the programme committee, the participants and above all our hosts, Prof. Simon Lin and his excellent support team at Academia Sinica.

Robert Jones conclusions about ISGC 2010

Bob Jones is the EGEE-III Project Director.
Here are his conclusions about ISGC 2010:

The grid-treatment

This morning I've been sitting in the biomed session on the last day of ISGC2010. Among the talks was a presentation on research EUAsiaGrid is supporting into Dengue fever.

I spoke to Ying-Ta Wu, one of the brains behind the project, about this yesterday. As an associate research professor in the Genomics Research Centre in Academia Sinica, Wu's main responsibility is in drug screening. He is searching for a small molecule or compound that will interact and inhibit NS3, a protein which is important for Dengue virus proliferation.

Read on below to find out what he said (and also take a look at this great article on the subject in iSGTW this week).

GridCast: Why have you chosen to study Dengue fever?
Wu: Currently there's no drug available for Dengue fever apart from traditional medicines that are not based on scientific research. Dengue is not a top priority for pharmaceutical companies because it is regional and only occurs in developing and under developed countries which are not considered to be a big market.

GC: How would researchers usually find new drugs?
W: Usually in drug discovery, researchers would expression this protein and set up an assay protocol to measure the protein's activity. If a molecule interacts with this protein, it would reduce its activity.  That would all be done in the wet lab.

GC: What are the problems with this?
W: There are many many compounds available so it's very expensive and it's not a very good idea to test each individual compound one by one. So you need to have some strategy. In the Genomics Research Centre we have a big automatic screening system – a robotic system – which can screen a large amount of compounds a day. But even so, it's very costly and takes a lot of time to prepare and do the work.

GC: What approach are you taking?
W: In this anti Dengue virus project we're taking another strategy where we do virtual screening before the wet lab. Instead of doing the wet lab experiments, we are modelling the interaction of individual compounds with NS3 and from there then we measure and compute their interaction energy. We select compounds which have a very good interaction with the protein - we call it a 'potential hit.' We then analyse those potential compound structures to extract information about the structure. That information we submit to the chemist and they will synthesise a drug based on that information.

GC: What are your results so far?
W: We have already screened 300 000 compounds, and have got about 2000 potential hits. Those hits can be clustered based on their structure and similarity into 183 groups. Groups with large member sizes and with high average interaction energies are then suggested to the medicinal chemists.

We've already submitted that information to the biologists and chemists we're working with. Our collaborator Dr Doman Kim from Korea, uses this information for assays in the wet lab. He's started this but we haven't got the results yet.

GC: What tools are you using to carry out the virtual screening?
W: The tool we're using is called GVSS developed by EUAsiaGrid. On this platform the participants can submit their own library [of compounds to test]. If they don't have their own library we can prepare one for them. But we really encourage more people to join us and submit their own libraries or even other targets – all they need is the protein data bank information.

The beautiful thing about GVSS is that even people who don't know about computational methods can easily submit their job. For people doing the virtual screening, we have to screen a lot of compounds. It's very difficult to set up, because you have to prepare a lot of compounds you have to prepare the target and then most of all ,you have to find enough CPUs, enough resources.  Even if you do have enough CPUs you don't know how to submit the screening on a big scale. With GVSS all you do is click the target, decide the compound and just submit.

GC: What are the benefits of using this method?
W: I think the benefit is we can actually have more people in this area join the work against fighting a common disease. They can share their library, their data and their computer hours once they join EUAsiaGrid. We're currently collaborating with groups from Vietnam, the Philippines, Malaysia, Indonesia, Korea of course Taiwan!

If users are interested in any other disease or any other target they can submit their target to GVSS too, they just need the PDB file of the target. The exciting thing is we can have people gear up to fight those less interesting targets of pharmaceutical companies.

GC: So what's next?
W:I think the next step is to wait for the data and then we'll try to see what we can adjust the virtual screening model accordingly. We would like to get more and more people to know about this platform so we can form a power source to work towards the same target.

An introduction to social simulation

As mentioned in earlier blog posts, one of the first sessions at ISGC 2010 was a full day tutorial on social simulation.

But what exactly is social simulation? Alex Voss explains in the video below..



You can find out more about social simulation here.

ASIA@home satellite event in Beijing

On Monday, three of the ISGC participants headed north to Beijing for a special satellite event there.

It used to be that to get from Taipei to Beijing you had to transit via Hong Kong, and the trip would take most of a day. But since 2008, there are direct flights between the two cities, so the trip takes just three hours. In fact, there is a great deal of collaboration between researchers in Taiwan and on the mainland. As is often the case, scientific exchange has helped pave the way for better political relations.

In that spirit, we held a satellite Asia@Home event on Tuesday at the Institute of High Energy Physics, which is part of the Chinese Academy of Sciences. Dubbed CAS@Home, this was a follow-up on an Asia@home seminar held nearly a year ago in Beijing, as another ISGC satellite event, which was designed to stimulate interest in CAS for volunteer computing and BOINC.

Derrick Kondo (INRIA) and Daniel Lombraña González (U. Extremadura) kicked off the session with two introductory talks in an open session, and then we moved to a smaller venue for the real master class session. There, several researchers from different institutes of CAS as well as from Tsinghua University presented projects that they may want to adapt to volunteer computing.

There were over 20 participants, and ideas ranged from using graphical processor units to speed up high energy physics calculations (Niklaus Berger of IHEP showed some very promising results for this), as well as some biotech and nanotech applications, and even an interesting proposal to use volunteer computing to automatically extract semantic and ontological information from Chinese texts, from Zhao Juan of the Chinese Computer Network Centre.

In the afternoon, Daniel led a hands-on session in how to install both the BOINC client and BOINC server software, with an example of a molecular dynamics code for nanotech research supplied by researchers from Tsinghua University. Daniel showed how you can get a project going in less than an hour. If you are Daniel, of course!

Ben Segal from CERN joined by skype video to talk about CERNVM - the virtual machine initiative for physics computing - and combining it with BOINC. This is of interest for high energy physicists in Beijing, where the BESIII detector is producing a lot of data these days. Derrick Kondo wrapped up with a tutorial on how to install a BOINC server on the Amazon EC2 cloud - very easy provided you have a credit card :)

There was considerable interest in Daniel's Jarifa project in Extremadura, as a way to manage volunteer computing within an institution. Deploying volunteer computing within CAS institutions, of which there are over 113 throughout China, seems a promising way to better exploit the significant idle resources in desktops and laptops that belong to such institutions.

After all, not all research needs the tens of thousands of volunteer processors that keep projects like Einstein@Home and ClimatePrediction.net chugging along. And campus grids using idle desktop resources could also be a good way to reduce the workload on central computing resources, providing savings for each institution.

Chinese hospitality is always great, north or south, and the master class ended with a delicious dinner for some of the participants and teachers. You can see them here. I don't have a fancy panoramic camera like some of my co-bloggers on this GridCast, so this 360 video was taken using a very advanced technology: place your video camera on the centre of the rotating tables that are used in Chinese restaurants to share the food... and turn!

A Walk in the Sunshine

This is Andy Turner's fifth in a series of GridCast posts about ISGC 2010. His previous post is here. It is my penultimate post, the final one I will write once I am back in the UK.

After a morning swim I sat down to breakfast with friends and we talked about matters of research and the future, reflected on the annual series of ISGC events and its focus and wondered how to make the most of our time here now and if we come again. It was one of those spinning conversations that touched on yin yangs of philosophy, mathematics, logic, the humanities, social sciences, and considered life and art of being a good researcher and a good person generally.

Our time here is to some extent what we make of it, but what is arguably as important as attending sessions is making connections both with delegates and others in Taiwan and not missing the opportunity to enjoy this place and its people. With this in mind, I arrived at the Building for Humanities and Social Sciences hopeful of finding a friend to join me on the short walk I suggested in the post I made before I arrived in Taiwan. I uploaded some photos from the walk which you can find linked here. We chatted with a nice fellow at the top who looks after the trail. He was there studying some wildlife and was surely pleased that we had come to enjoy the place he helped make.

More from me from the day can be found here.

ISGC 2010: Alexander Voss' talking

Alexander Voss is a SICSA Advanced Research Fellow in the School of Computer Science, University of St Andrews

ISGC 2010: Royol CHITRADON on climate prediction

Royol CHITRADON is the director of Hydro and Agro Informatics Institute in Thailand (HAII).
In this video, he is explaining on what they are currently working: climate prediction.

Their observations for this year are a bit worrying, and we would take care about what they discovered...

Steven Newhouse talks about grid relations between Europe and Asia

Steven Newhouse is the Technical Director of EGEE-III Project. He is also the Project Director of EGI-InSPIRE Project, which is starting in May 2010.

Shaking up earthquake research

Later today the afternoon session at ISGC will focus on earth science and disaster mitigation. As I mentioned in a post right at the start of ISGC I attended a disaster mitigation workshop on Sunday which looked at how we can limit the damage caused by earthquakes. Coincidentally, the workshop took place just days after a 6.5 magnitude earthquake hit southern Taiwan. (The picture below shows the main shock and after shock distribution for the 4 March 2010 Earthquake. Click to enlarge)

As promised here's what I found out from the scientists at Academia Sinica involved in this research:

“Earthquake prediction is an unsolved problem. But using data gathered by seismometers we are able to predict ground motion and reduce the damage. Providing access to earthquake data will help the Asia-Pacific to be better prepared when an earthquake strikes - the more information we have, the better.” says Li Zhao from the Institute of Earth Sciences, Academia Sinica, Taipei.

“Our dream is to have  an integrated regional data centre for the Asia-Pacific, which is accessible for scientists to study the earth nature.” says Wen-Tzong Liang also of the Institute of Earth Sciences. This could improve scientist's knowledge of earthquakes and the earth's interior, providing information for engineers to design and reinforce buildings appropriately as well as teaching citizens how to respond when an earthquake strikes.

In order for such a network to be successful, data needs to be gathered from countries across the Asia-Pacific, not just those that are prone to earthquakes. The team at Academia Sinica, led by Bor-Shouh Huang, have already started tackling this problem. In the last two years they have set up ten new stations along the Vietnamese coast, and are set to deploy even more in the Philippines.

These seismic stations will produce real-time data continuously for any local data centre to monitor earthquake activity in this region. Giving scientists wider access to the archived data can help them predict what will happen when an earthquake strikes and understand what the earth structure is below the surface.

“We use computers to simulate wave propagation so if there's an earthquake in Taiwan we can determine how much the earth will shake anywhere in the world.” says Li Zhao from the Institute of Earth Sciences, Academia Sinica. “Using archived data records we can investigate the structure inside the earth, and if we know this we can better predict the ground motion. For example Taipei lies in a basin – the ground is covered by a soft sedimentary layer. So if an earthquake happens, Taipei will experience a higher motion than the surrounding area, a process called amplification.”

To set up this network, researchers are hoping grid technologies can provide robust and reliable ways to transmit and store data. They have already turned to grid computing to help analyse the data itself.

“The most important ground motion is in the frequency of a few Hertz, so the higher the frequency the more realistic the prediction is. But doing calculations at very high frequency requires a lot of computing power. Grid technology gives any researcher with an internet connection a way to run simulations for any earthquake they wish to study.” says Zhao. Researchers demonstrated this gateway at the ISGC 2010 workshop earlier this week.

For more info on this research keep a look out for a story coming up in iSGTW next week. In the meantime why don't you head over to this week's iSGTW, which is a special ISGC All-Asia issue.

ISGC 2010 Secretariat cares about you

Feeling cold?
We make you warm.



Feeling Hot?
We make you even HOTTER !!

Taipei by night

ISGC 2010 is happening now in Taipei. But around this great event, you may discover the town, especially by night...

From Infrastructure towards Applications Research

This is Andy Turner's forth in a series of GridCast posts about ISGC 2010. His previous post is here.

Day 1 of the main conference began with an opening ceremony and a set of 3 keynote speeches about infrastructure. With the failure of my alarm clock batteries and a sleepy head I was late, but listened to Steven Newhouse present about EGI. Steven is one of the GridCast team at ISGC 2010. I said hello to him later after we left a sumptuous reception, but I don't think he recognised me. Prior to the reception, which was a posh sit down meal, I was trying to catch up all day after being late and upon arrival back at my accommodation my worry was more about the state of my paper and presentation slides for the next day, so there was no GridCast post from me yesterday.

Today was Day 2 of the main conference which began with another set of keynote presentations and an air of transition from talk mainly about infrastructure to talk more about enabled research applications. The session began with more of an infrastructure presentation delivered by Bernard Marachel about South American grids and their sustainability and linkage with other grids. (I guess Bernard, who travelled here from Brazil, is the delegate that has had the longest journey of anyone to be here. At lunch our chat strengthened this theory as Bernard reckoned it was at least 20000km in any direction from his home to here.) Next came a presentation by Rob Procter about activities in what has been termed e-Social Science in the UK some of which I have been involved in. One thing Rob said chimed in nicely with what Mingchao Ma said yesterday in the Grid Security and Networking I Session: that is that the infrastructure is people and so investing in people is very important. I appreciate those kinds of sentiments, people are generally the most important part of an organisation.

The final keynote was my favourite talk of the session. It was about e-Wissenschaft and was presented by Tobias Blanke. It was funny and informative and witty and thought provoking. We are on our way to data driven research in the humanities and social sciences and we have a virtual infrastructure called the Digital Research Infrastructure for the Arts and Humanities (DARIAH) to support us. DARIAH is an organisation aware of the importance of people in establishing its connections, indeed many of its connections are in the form of liaison between people.

More from me from the day can be found here.

Marco Paganoni's talk

Marco Paganoni, from the University of Milano-Bicocca, is the Project Manager of the EUSIAGRID Project, and he is working for INFN too.
He is talking about the projects he is involved in, and how he discovered the grid computing worlds...

The best little dumpling house in Taipei

So, two nights ago about seven of us went with some of our Taiwan hosts to a little restaurant near Taipei City Hall that had the most extraordinary dumplings.

Today, I learned that it is famous throughout Taipei, and a major stop for all tourists (most of whom, for some reason, are from Japan).

Called "Din Tai Fung," it usually has an enormous line out front, but maybe because it was a weeknight, there was only about a 10-minute wait.

They have about a dozen different kinds of dumplings, and yes, Virginia, there is a difference between each of them: with hot chili sauce, crabmeat, vegetables . . . But whatever the variety, our hosts said the secret is the juiciness.

The price was pretty good too -- only the equivalent of 10 euros per person for several courses, includng wine, beer and dessert. (In other words, an entire meal for less than the price of a small pizza in Geneva!)

Be sure to try the red bean paste cake, which was apparently Madame Chiang Kai-Shek's favorite dessert.

And try the "Shaoseng" wine, if you dare. It's served warm . . . with dried plums or slices of lime dropped in the glass and allowed to steep. My French companions were shocked at first -- but then asked for more.


PS -- We also learned about the hidden meaning of chopstick handling: if a woman holds them so that her fingers are very close to the plate, that means she will marry very close to home. If she holds them so that her fingers are far away, then she will marry far away.

No word on whether there is an equivalent for us guys. But given our extraordinarily attractive waitresses, we agreed we'd be tempted to marry far from Geneva . . .

Behind the scenes

And here's an image from the Lingnan Fine Arts Museum that our photographer forgot -- perhaps because it is not "fine art?"

Wide image of Welcome Reception

I would like to share the wide image of welcome reception as well. :)

ISGC 2010 welcome reception

Here are some welcome reception photos :

The unique design for ISGC 2010 in the Tiger Year, hope you all would LOVE it!