Well, today marks my ninth day at PSC, and the beginning of my second full week. Haven’t jumped the shark yet, glad to say.

I’m also glad to say it’s been busy. There’s a lot going on at PSC, some of which I can share now and some of which I’ll hopefully be able to share in the not-too-distant. As far as the former:

Amber Leigh Harmon, the new writer at International Science Grid This Week, is picking up on Michael Schneider’s piece about using supercomputer simulations to better understand aortic aneurysms – malformations of the heart’s mainline to the body. This topic is personal for me, because Sam Gulino, firefighter, a personal hero of mine, and my grandfather, died unexpectedly of a burst aneurysm when I was 13. It’s also nice to help out a good egg like Amber, who I met at SC12. I look forward to reading her story.
We’re also getting into gear for the Sherlock launch on Feb. 1. We’ll be sending out a release on this closer to the date, but it’s such a neat machine I’ll refer back to my blog from SC12.
In the “I had no idea” file, I just found out that PSC had a large role in the supercomputing behind today’s life-saving storm reports. Again, this has a personal angle for me. My family is from Hackensack, N.J., which saw a lifetime-event four-foot storm surge up the Hackensack River. Many of you may have already known this; much to my chagrin, when I told my wife, Heather, about it she said, “Yeah, I heard that in one of my podcasts a month ago.”

So much for Pittsburgh’s Voice of Supercomputing. I guess I still have a lot to learn.

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A double dose of congratulations is in order to our own Markus Dittrich.  In addition to being recently named the new Director of the National Resource for Biomedical Supercomputing (NRBSC) at PSC – a huge job in itself – he will also head PSC’s participation in the recently announced Center for Molecular Modeling of Biological Systems  (CMMBS), a partnership between the University of Pittsburgh School of Medicine, Carnegie Mellon University (CMU), and PSC.

Markus, who is originally from Germany, came to PSC in 2006 as a post-doctoral researcher with Joel Stiles.  He was promoted to senior scientific specialist, and then to group leader of NRBSC before becoming the director.  We talked recently  about CMMBS, and the NRBSC,  software development, and e-books vs. paper books.

Congratulations on your new position in NRBSC!

Thank you. NRBSC is doing well.  And as you know, we just became a major partner in the newly funded CMMBS, a Biomedical Technology Research Center from the National Institutes of Health together with the Department of Computational and Systems Biology at Pitt and the Lane Center for Computational Biology at CMU.

How does NRBSC fit into CMMBS?

As part of this new Center, NRBSC will continue its focus on computational biological research.  There are multiple levels in our work:  first, the atomic and molecular level simulations, then simulations on the level of cells, with many molecules, things like that.  Then there are even higher levels, tissues, and larger, organism-level things, and the large-scale volumetric image analysis that comes in there.

Art (Wetzel) and Greg (Hood) are part of the image analysis effort.  I personally lead the cell modeling aspect, with MCell development with invaluable work from Jacob Czech.

What else is going on in NRBSC?

There are lots of other research activities going on in NRBSC. For example, I have a successful collaboration with Steve Meriney at the University of Pittsburgh doing cell modeling and trying to understand the structure and function of synapses.

Besides research, we have the MARC program, which  is a very successful,  very important outreach mechanism, which  Hugh (Nicholas) and Alex (Ropelewski) established. It really helps minority institutions get their foot in the door.

We have lots of other outreach and training activities headed by Pallavi (Ishwad).

And there’s Anton.  We’ve been doing that for 2 years now and the project has been hugely successful.  Very recently, research that used Anton for its computational work was published in Nature.

We were just awarded a 2 year supplementary grant to continue Anton support here at the PSC, and D. E.  Shaw has agreed to leave the machine here for at least that long.  Hopefully we’ll be able to continue beyond that, of course, but 2 years is a good head start.

There’s lots of other things going on, and hopefully in the future we will continue to get involved in new and exciting collaborations and new projects.

What kind of work are you and Steve Meriney doing with synapses?

We are studying structure and function in synapses. Steve is an experimental neuroscientist at Pitt.  So we combine his experimental work and my simulation work  to develop models  to understand more and more how these systems work. 

It’s important for this type of work that you combine simulation and experiment.

How do simulations and experiments work together?

Simulations allow you to get insight that you can’t get using experiments, because many of these synapses are not accessible experimentally.  It’s very difficult to look at very detailed events in an experiment, but it’s easy in an MCell simulation.

On the other hand, to make a successful simulation, you need a lot of insight from experiment of how those systems work, to really build a model that you can trust.

It develops in a synergistic way: you build a model, then get input from experiment,  and you build from there.  Right now, we have a nice model developed that seems to agree quite well with what you see in experiments. It’s really quite predictive.  So we are excited to use that, to actually explore new avenues using it.

So your educational background is in biology? or in computer science?

Well, my way, way, background is physics.  I went to the University of Regensburg  and got a diploma in physics.  That’s equivalent to a master’s degree, maybe, here.  I focused mostly on theoretical condensed matter physics, understanding materials.

Then I went to the University of Illinois at Urbana-Champaign (UIUC), and joined Klaus Schulten’s group, who is a big name in the field of molecular dynamics simulations.  So doing my PhD, that’s where I got into the life sciences, and using computer simulations to understand how living systems work.  To me, that was, really, I don’t if it was life-changing, but it was really fantastic to use these physics based approaches to understand living systems.  It’s very different than material science, a whole different kind of beast to tackle. So it was really great fun.  I enjoyed it a lot, and I’ve been doing biophysics, I guess, ever since.

And that’s when you came to the States?

Well,  I went to college in Bavaria, and the University I went to had an exchange program with UIUC. So I went for a year to the States, I believe it was in ’97, and spent a year at the physics department there.  I didn’t  have any contact with Klaus at this point.  But that’s where I actually met my wife, Susan.

I really liked it in Urbana-Champaign, it’s a really nice small town, and a fun town to be in.  So I decided that I wanted to go back and do my PhD there.

 What brought you to PSC?

Well, when I did my PhD, I mostly focused on enzyme structure and function, particularly on one enzyme called F1-ATP synthase, which is a quite famous protein.  It’s a nice machine. A molecular motor.  You feed it a chemical called ATP and it converts that chemical energy into mechanical rotations. It’s a wonderful example of  something nature has come up with to make life work.

After my PhD, I felt like it would be good for me to also see some other type of approaches to simulate biological systems, so I got in touch with Joel Stiles.  I knew I wanted to do some type of cell level simulation, and he was a pretty well-known person in that field.

Once I got here, I went from just studying single molecules to  studying whole cells and sub-cellular systems, synapses in this case.  It has been great to see different aspects and to learn new tools. It helps you to get a much better view of how to look at systems, to have a repertoire of methodologies that you can draw on  to approach them and to try to understand them. It’s really nice  to understand how things work.

Between your research and being the director of NRBSC, you must be very busy. Do you do anything  for fun?

I do a lot of running, although I’ve been slacking.   I used to run every day, but now it’s down to four or five times a week.  I’ll get back to every day eventually.

Also, I do a lot of programming just for fun.  I enjoy it, so as a hobby, I spend most of my time coding.   I do a lot of reading, too.

What are you coding?

All sorts of stuff.   My wife is a knitter, so I’ve started writing some software for her to create knitting charts, called sconcho, that’s on SourceForge.

And what are you reading?

I usually go to Project Guttenburg and look at those books.  I started re-reading some of the books I read as a child, and right now I’m reading “The Last of the Mohicans” on my Kindle.

Do you still buy physical books?

I do, but I’ve reduced it a little bit.  I’m sort of a book nerd.  I have a pile of books that are unread.  I keep buying them and I keep cursing at myself for doing it.

I still prefer technical books as physical books.  I think the Kindle, to just read a novel, it’s fine.  But it’s inconvenient on a technical book that you have to flip back and forth a lot, and you have little notes in there and things, it’s hard to work. It’s different from having a physical book in your hands.   Then again, you only have so much space in your house, right?  It’s good that the e-books are not really taking up any space on your bookshelves.

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A group of high school students were touring SC12 on Wednesday afternoon, and the PSC booth was one of their scheduled stops. I figured I’d tag along with one of the groups; see what they were interested in, maybe get a cute quote or two.

The afternoon began with a talk by Henry Neeman of the University of Oklahoma, “What the Heck Is Supercomputing?” I’m a little embarrassed to admit that I found its content to be much more at my level than Sunday’s Basics of Supercomputing.

He gave me a better appreciation of what the world looks like outside Pittsburgh. We’ve developed a niche in shared memory machines, of course. But it’s useful nevertheless to take a look at why there are shared memory and distributed memory machines, the logic behind both.

Neeman set a couple of the students at assembling a 1,000-piece jigsaw puzzle, showing how, if they shared the pieces, they’d invariably wind up getting in each others’ way — contention, in the supercomputing idiom.

It was a beautiful illustration of why distributed memory machines, with thousands to millions of core processors, work as well as they do. If you don’t give the cores access to the same bits of the memory, they can’t come into conflict accessing them. This allows you the vast power of having all those processors work parts of the problem in parallel, getting the job done in a fraction of the time. (As always, beware of my simplifications for clarity. There’s more to it, of course; but this will do for a first level of understanding.)

Neeman was quick to mention a big downside of distributed memory computing, one I’d heard mentioned before but hadn’t fully appreciated: When you write such a parallel program, you can’t just write it for the job at hand. You also have to explain to the machine how to split up the work between all those processors. That bumps the level of difficulty up to apply-head-to-desk-repeatedly levels.

So that’s two reasons why a particular problem might be better tackled by a shared memory machine like PSC’s Blacklight or Sherlock, in which a smaller number of processors share all the memory: datasets that can’t be worked on in pieces (see Fresh Fish), and problems whose investigators don’t see the time and effort of parallel programming as cost-effective. Not surprisingly, different architectures turn out to be better for different problems.

What really won me over, though, was a brief reference Neeman made to chaos theory. I hadn’t heard the term in 25 years, and it marked him and me as part of the same tribe. (I actually managed to shoehorn a reference to chaos theory into my dissertation; nobody on the committee mentioned it, so I suppose it was apt, or at least innocuous. Today people tend to cite “complexity” rather than chaos, and actually know what they’re talking about.)

After the talk, the high schoolers split into groups, each to be led by an SC12 student volunteer. I tagged along with about a dozen kids from the same school in Salt Lake City, partly because they were wearing school T-shirts and sweatshirts and I figured I’d be less likely to lose them (OK — myself).

What no one counted on was the effect of filing a bunch of teen geeks into a cavernous, deafening convention center full of gadgets. The moment we hit the open space, they scattered like cockroaches caught by the kitchen light (hey, I’ve lived in the South Side of Chicago). The teachers and I looked at each other, mouths hanging open: no real option but to forge on with the two students left to us.

The clock, however, was against us. The whole shebang had been creeping more and more behind schedule, and at 5:21 one of the teachers announced that they needed to bug out to make their bus.

We weren’t anywhere near the PSC booth, of course. Leaving the teachers to the unenviable task of collecting their students, I rushed to the booth to see if I could intercept another group. I did, though just barely: a group of three adults and one student — a quiet girl who didn’t say much — swung by, and John Urbanic ran them through PSC’s machines and what they do. I mostly lurked as the tour wound down, wondering where all those students had gotten to, and what the heck I was going to write about.

Chaos, as usual, getting the last laugh.

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Where do you think I met Steve Brandt, of Louisiana State University’s Center for Computation & Technology?

We’ll get back to that; in the meantime, I guess I should say who I am. I’m Ken Chiacchia, and in January I’ll start as PSC’s senior science writer. I was trained as a biologist, but never really liked the laboratory life. So I chucked it all to pursue literary pretensions: science writing, newspaper reporting, even a little science fiction …

Bottom line is, “computer scientist” ain’t anywhere in there. I’m here at SC12 to soak up as much as I can, fresh fish that I am. On Monday, I went to Steve’s workshop with Thomas Sterling of Indiana University, “A Beginners Gude to Supercomputing.” I also talked with Nick Nystrom, PSC’s director of strategic applications, about our new machine, Sherlock.  (See some neat pics of Sherlock’s installation, via Robin Flaus, here.

No, the workshop isn’t where I met Steve. Bear with me.

Supercomputers fit on a spectrum defined in part by how much memory is available to each processor. The simplest kind of distributed memory machine, the most common type of supercomputer, has many core processors, each of which has access to only a small part of the dataset. They generally work best on problems that can be split into many parts that can be worked on separately. Shared memory machines have fewer processors that have access to the whole shebang, and are best for problems that can’t be split up efficiently.

Now that’s an oversimplification: there are distributed memory machines with powerful connections between their processor/memory units, but at a certain point the dataset is so hard to split up that you need shared memory to avoid the computer spending lots of time just trading information between its processors rather than calculating.

Sherlock is a shared memory machine. But it does something very important in addition — and it’s all about relationships.

Let’s say you wanted to find out who I have in common with Steve Brandt by searching our Google contacts. It rapidly becomes a big problem, because of the “seven degrees of separation” rule (exclude the quick connects via supercomputing folks; that isn’t it). Worse, the connections between people are arbitrary, making the dataset notoriously difficult to split up. If you try, you inevitably break connections that you need to follow, which makes them difficult for a distributed memory machine to work efficiently.

Graph datasets consist of nodes — people, in our example — and edges — connections via Google contacts. On a vastly larger scale than our example, graph analysis is the same problem faced by a molecular biologist trying to overlap thousands of tiny DNA fragments to amass an organism’s genome. Or a government disease control agency, trying to analyze how social networks can spread misinformation that undermines their efforts to minimize an epidemic. Or an astrophysicist, trying to find clusters of galaxies in the Sloan Digital Sky Survey.

But the trick is, even a traditional shared memory machine will have some trouble with this kind of calculation. Every time it chases down a connection — every person I know in turn knows multiple other people, and each is a lead that needs to be followed. Sherlock tackles this with something called massive multithreading — each core processor can take on many leads at once.

It’s much like, having found that a person I know in turn knows five people, you called in five friends, each to chase down one of those leads. A typical shared memory machine has two to at most four hardware threads per processor; Sherlock’s 64 paired processors have 128 each.

So let’s say you run though Steve and my Google contacts and find an interesting entry for each — in mine, it’s St. Gregory Roman Catholic Church, Zelienople, PA. In Steve’s, you find a parish in the Baton Rouge area.

Aha. Following up on this lead, Google maps tells you that Sacred Heart Catholic Church is on East 9th Street South in Salt Lake City, about two miles from the Salt Palace Convention Center. A quick check on our smartphone GPS logs, and you’d find us converging at Sacred Heart at 9:30 on Sunday morning.

Now you know where we met; you also know something else we have in common. (OK — you could have just looked at the GPS logs to begin with. Still, you get the idea.) Importantly, it came through checking out a nonexplicit potential connection in the dataset — which is the kind of problem, writ vastly larger, that Sherlock has been designed to tackle.

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We recently welcomed Nate Robinson to the PSC team as our newest, and coincidentally youngest, network engineer.  Nate comes from a small town in central Pennsylvania whose county boasts only one stoplight. Yes, that’s one in the entire county!  He left his small town to attend Slippery Rock University of Pennsylvania  in the slightly larger town of Slippery Rock, PA .

While there, Nate was involved in campus life, including the Ultimate Frisbee and Computer Technology Clubs.  As a member of the Computer Technology Club, Nate discovered PSC by attending our annual Discover Open House. (And we caught him… check out the third photo from the left!) He made a particular connection with networking staffers Steve Cunningham and Shane Filus who explained the various research and networking projects going on here.   So when Nate started the hunt for his first job after college, he looked for an opening at PSC.

He has already embraced many new experiences living here in the big city, like trying Indian food for the first time. “I really can’t compare it to anything I’ve eaten because of how vastly different it tastes. It was scrumptious, but as far as a comparison goes, it just simply was. I’ll be ordering it for lunch in the future for sure,” he says.

In his first “real” job, he says he’s been exposed to “some pretty amazing technology”. But his favorite part of the job, Nate says, is the environment. “I like that I can get work done and be silly and have fun doing it.  And all of my co-workers are awesome.”

He successfully ran his first pairs of  fiber optic cable recently.  “I think the hardest part was making sure that I wasn’t too rough with the fiber while maneuvering around in the ceiling,” he laughs. “I may have been a little too delicate, but in my eyes I was holding a newborn baby and I didn’t want to break it. ”

Another big first is looming.  Next week is his dreaded first week of “pager duty” – being on call for  network emergencies.  He says that he is nervous, “but at least I won’t have to deal with Hurricane Sandy.”

Nate, we know you’ll do a great job even if Sandy’s twin rolls in.  Welcome to PSC!

 

 

 

 

 

 

 

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Just in time for Halloween comes this call for research into a neglected field of public health.  Here’s an excerpt from the latest Supercourse newsletter by Ron LaPorte which asks the question:  Why is there no funding for public health research on Zombies?

Zombie Flesh Eating Epidemiology

I could find no epidemiologic literature on zombies. (http://en.wikipedia.org/wiki/Zombie).

Ron LaPorte

Ron LaPorte

Halloween is a big night for Zombies as they all come out, kill people and eat their brains and flesh. Clearly Zombies are a major risk factor for death, yet to my knowledge there has never been a zombie case control study, or prospective study. We do not even know the prevalence or incidence of Zombies, nor natural history. Moreover there is no Zombie Institute at the NIH. Just in terms of anecdotal information (e.g. the Night of the living dead) the Zombies appear to be very lethal. At is amazing that there are over 24000 articles and millions of dollars investigating flesh eating bacteria, but almost no money spent for flesh eating Zombies, this must stop. I think there may even be some active discrimination against the epidemiology study of Zombies. Raj Bhopal has never had a epidemiology of Zombie sessions at the IEA meetings. We are not alone; our basic research friends have never produced a simian or rat model of zombism. Zombie epidemiology is new paradigm. However, there are several major methodological issues that we epidemiologists need to resolve. How do we calculate a mortality rate of zombies die twice? Also in our Cox Regression model people are either classified as alive (0) or dead (1). What do we do with a zombie who is “living dead”. It is a puzzle. Perhaps we should code Zombies as .5. Also, is it legal to censor someone twice from a life table? We can make a brand new field, and hopefully will see some RFPs in this area.

It appears that there is an infectious etiology to becoming a Zombie as if you are bitten by a Zombie, you may become a Zombie. On could speculate further that this is a “bite” is transmitting prions. Also, it has to be related to hygiene as you cannot be buried for years without becoming a little dirty. Psychiatric Epidemiology plays a role as Zombies appear to have mood disorder.

It is also disappointing that no one has followed up on a very important lead. We know that with Creutzfeldt–Jakob disease there appears to be transmitted as the result of eating brains, and similarly potted head eating in the Shetland Islands is associated with MS. The favorite food of Zombies is human brains, yet no one to my knowledge has pursued this hypothesis.

“Great minds Taste Alike” (Zombie quote)

We should start Zombie Epidemiology in Pittsburgh. My city started the identification of the infestation of Zombie epidemiology. This all began the Monroeville Mall in 1968. http://en.wikipedia.org/wiki/Night_of_the_Living_Dead It was here, that the classic 1970s movie was filmed “The Night of the Living Dead” which started the zombie epidemic. If you come we can arrange personal tours to show you the birth place and the first death place and second death place for Zombies. See below the trailer for the movie (do not look at this if you are afraid of Zombies) http://www.youtube.com/watch?v=pElSu_ECJGM

Primary Prevention

As we know so little about prevention of death by zombies, it is difficult to give advice as to how to avoid having your brain eaten. One piece of prevention advice is exercise. Every Zombie I have seen is a very slow walker. With a little exercise who should easily be able to out run them. Also, if they start to attack, make sure you in front of the slowest person who looks like a nerd with a big brain.

As we all finish our articles, clearly more work is needed in this area.

Thanks to Ron LaPorte and the entire Supercourse team for taking up this cause!

The University of Pittsburgh Supercourse is dedicated to improving global health by sharing knowledge.   Visit the Supercourse web site to  get up-to-date public health information, and share some of your own expertise with the rest of the world.

To get monthly updates on global health issues, subscribe to the Supercourse newsletter by emailing the Supercourse team at super1@pitt.edu.

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We just finished reviewing the results of the XSEDE User Satisfaction survey, and we hear you loud and clear.  Thanks for the many compliments, and also for your suggestions about how we can improve. We’ll be changing our practices where necessary in line with your ideas to make your research run more smoothly and productively.

We are still looking into all the ways we can be better,  but we are committed to these improvements:

  • Documentation aimed at both helping less experienced users get started with high-performance computing and enabling experienced users to get their work done quickly and efficiently
  • Clear and specific information on job scheduling
  • Tools to enable you to see the status of your jobs
  • Easily accessible information about Blacklight’s operational status

We expect to come up with more ideas for improving your experience at PSC in the coming months, and we’ll let you know about those as we implement them.  Keep the suggestions and comments coming – you can contact us any time via our feedback form.

 

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For more than ten years, PSC has been reaching out to minority-serving institutions (MSI) with bioinformatics training. This year, the annual MARC (Minority Access to Research Careers) program at PSC began with a nine-day workshop in June. The interns, who were undergraduates, graduate students, and even a faculty member this year, stayed for a seven-week internship where they applied their new bioinformatics skills to a research question.

Although they’ve all left for home, we could not forget this bunch. We want to brag about the interesting research that the interns did with their PSC mentors, Dr. Hugh Nicholas, Alex Ropelewski, and Dr. Troy Wymore.  So, in the next few posts,  we’ll present the the 2012 MARC summer interns and their projects.  First up, the undergraduates:

Angela McClendon will be a senior at Jackson State University this fall, majoring in chemistry and biology.  That’s a great background for her intended career in pharmacy, and that ties in nicely with her MARC project.   Working with Troy, she studied sensor proteins that contribute to antibiotic resistance in bacteria.

Specifically, she was hoping to pinpoint some differences between a protein known as BlaR (pronounced blah-are) and β-lactamases, enzymes which attack β-lactam antibiotics.  (The β-lactam class of antibiotics contains penicillin derivatives and cephalosporins, among others.)

The sensing proteins, like BlaR, are structurally very similar to β-lactamases.  So why does BlaR have very little effect on β-lactam antibiotics, when β-lactamases destroy them?

Using phylogenetic analysis, Angela was able to pinpoint differences in the amino acid residues of BlaR and β-lactamases that most distinguish the proteins from the enzymes. She had no experience in bioinformatics before this summer.  “I learned a lot about bioinformatics,” she says.  “I learned how to align sequences, how to annotate a protein structure, how to make a phylogenetic tree.”

Angela also found many differences between Jackson, Mississippi and Pittsburgh.  One difference in particular really makes her shake her head:  “We do not ride our bikes in traffic,” she laughs.

Alexandra Medina, a senior studying microbiology at the University of Puerto Rico, Mayagüez campus, was also looking at the problem of antibiotic-resistant bacteria. Her adviser there, Dr. Carlos Rodriguez Minguela, is interested in GES-21, a β-lactamase that was found in waste waters in Puerto Rico. This summer Alexandra hoped to identify residues in GES-21 and other closely related β-lactamases that can be useful to predicting their functionality.

With no background, though, she first had to learn something about bioinformatics. “These two months have been hard, but I have learned a lot,” she says.

She started by finding enzymes with similar sequences to GES-21, and after using several software packages to eliminate extraneous sequences, align the remaining sequences, find patterns among them, and then refine the alignment, she was able to produce a phylogenetic tree showing evolutionary relationships between GES-21 and other β-lactamases.

She was also able to identify several amino acid residues common to the group containing GES-21 and a closely related group. (β-lactamases are grouped based on nucleotide and amino acid sequences.) The residues that she found are critical for the specific functionality of those groups and distinguish those groups from other groups of β-lactamases.

This can be really useful in fighting antibiotic resistant bacteria. GES-21, says Alexandra, makes bacteria resistant to a class of antibiotics called carbopenames.

“[Carbopenames] are used in hospitals and medical treatment as a last resort,” she says, because they are unaffected by most of the enzymes produced by bacteria. GES-21, however, is an exception; it attacks carbopenames and reduces the antibiotic’s effectiveness. Finding out what makes enzymes like GES-21 different could lead to a way to counteract its effect on carbopenames – extremely useful information in a clinical setting.

Has she learned anything besides bioinformatics in her stay here? “Oh my, everything!” she says. “I have never spent so much time alone, so I have been trying to get around on the buses – try to venture out myself , expand my boundaries, be a little bit more independent.” At least one thing she learned will surprise her parents. “I’ve learned to cook a little bit. Now I can make chicken and rice!”

Charnelle Smoak had to overcome not only a change of environment but also a change, essentially, in language.  A junior studying computer science at North Carolina A & T University, she had little background in biology.  “When I first came here, I had to figure out what multiple sequence alignment was! It was confusing for me at first, but when they started speaking Python (a computer programming language), I understood that.”

Her project, mentored by Alex Ropelewski, was to write a better multiple sequence alignment (MSA) program.  “The method is fairly simple,” she says.  “I break the alignment up based on motifs.  Motifs are conserved residues that the MEME program – that’s the one that I’m using – picks out, and these residues are important because they’ve been conserved [through the evolutionary process] for functional or structural tasks.”

Once the motifs are identified, those already aligned by the MEME program are set aside.  Charnelle’s program does a separate alignment on what remains.  Then those new alignments are stitched back together around the MEME motifs, to create a better MSA.

“I thought I would just learn a whole bunch of biology from this internship, but I’ve learned a lot.   I learned some things through the workshop that have nothing to do with my project, but are useful to me as a computer scientist,” like Unix and SQL and some intricacies of Python, she says.

She thinks of computer science as a key.  “In computer science, you learn a lot more than just computer science, because you are going to have clients of all different types. You might have a client that wants a program that does calculus, there might be one like this one that does biology, whatever it is, you have to learn at least a minimum [about the subject matter] to make the program to its specifications.”

She definitely plans to go to graduate school. “I want to become Dr. Smoak,” she says.

And apparently a crash course in bioinformatics wasn’t enough new skills for one summer.  One of the other interns also introduced her to salsa dancing.  “So I’ve been taking classes and learning how to salsa.  And I’ve been pleasantly surprised because I didn’t think I would be able to pick up any rhythm, I can’t dance whatsoever. But the instructor said, ‘You’ve improved so much.’ And I can actually do a little dance and almost look like a professional.”

As a native Pittsburgher, you’d expect Taylor Rosemond to have an easy time adjusting this summer.  But although she was literally right at home here, she had lots of new territory to explore.

Taylor is a senior applied math major at North Carolina A&T.  Her biology was a little rusty; no surprise, given that her last biology class was in 9th grade.  She had to do a lot of research on her own to come up to speed. “I read a lot of the papers that Dr.  Hugh gave me, and I did a lot of Googling, and I used the Encyclopedia Britannica online,” she says.

Then her intended project changed at the last minute.  Hugh and Dr. Gregory Goins, of the NC A&T department of biology, were planning to have Taylor develop a tool for biologists that would help categorize sequences into orthologs or paralogs.  “They found out maybe two weeks before I got here that someone had developed a package to do similar things,” Taylor says.  “So [my project] evolved into trying to use that package to see what kind of results it gives.”

The package that Taylor evaluated, bios2mds, can read in multiple sequence alignment files, calculate distance matrices, and perform metric multidimensional scaling.  Her testing  indicates that bio2mds can be a useful tool.

“What I have been doing is to look at the results it gives, and comparing it to the phylogenetic tree.  It gives you really good results,” she says.  “I think the largest alignment I’ve done is a little over 200 sequences.  It gives you groups that are all together on the phylogenetic tree. It’s a really accurate tool.”

Taylor plans to continue her education into graduate school, hoping to go straight  into a PhD program.  Although she’s not certain in what area, she thinks she would like to continue with applied mathematics.

Being in her hometown, Taylor should have had no surprises this summer, right? Not so. “I was telling the other interns that I lived in Pittsburgh my whole life, I went to St. Agnes School, down 5th Ave. (two miles from the PSC), and for high school I went to Oakland Catholic right on Craig Street (the same street that PSC is on, and just 3 blocks away) and I never knew this building existed.  In high school, we were all up and down this entire street, but  I never paid [the PSC building] any attention, that whole time. I thought that was pretty funny.”

UPDATE:  Congratulations to Taylor for winning an award for best poster presentation at the 2012 AGMUS Research Symposium.  Way to go, Taylor!

In the next post we’ll focus on the rest of the MARC interns and their research, including creating tastier guinea fowl, a clam with an unusual hemoglobin that carries sulfur instead of oxygen, and a family of bacterial proteins that may play an anti-aging role (at least in yeast).   Stay tuned!

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Things  have been busy at PSC this summer with lots of projects, workshops and supercomputing fun.  Last week a bunch of us made the 1 hour and 20 minute flight from the ‘Burgh to the Windy City to participate in XSEDE12, XSEDE’s annual conference.  We hunkered down at the historic InterContinental Hotel on the famous Magnificent Mile, to avoid the record high temperatures and soak in as much HPC goodness as we could.

Richard Tapia kicked things off as Keynote speaker; Tapia has an impressive resume as the Maxfield-Oshman Professor in Engineering and director of the Center for Excellence and Equity in Education, Rice University; director of the Empowering Leadership Alliance; and director of the XSEDE Scholars Program.  Dr. Tapia addressed attendees on “The Crisis in Higher Education:  the Need for New Leadership” which focused on the challenge that universities face to increase the participation of minorities in science, engineering and mathematics.

PSC staff participated in the conference in variety of ways. In addition to many of us attending the conference as participants, Phil Blood was on the planning committee as the Technical Program Chair.  PSC staffers also led a couple of tutorials and talks: John Urbanic presented a tutorial with Lars Koesterke from TACC entitled “Accelerator Programming with OpenACC and CUDA” and J. Ray Scott updated the XSEDE community on PSC’s new data storage solution, the Data Supercell.

Some of our students also participated in XSEDE’s student engagement program.  This program provides students with experience working on HPC-related projects across the various XSEDE partner sites.  PSC has three students working with us this summer as part of this program and each of them presented a short talk on their work during the conference.

The week ended with lunch and a surprising talk by Steven Reiner, Associate Professor of Broadcast Journalism at Stony Brook University.  Many of us didn’t expect a broadcast journalism professor to have a lot to say at a conference like XSEDE, including Reiner himself! But Mr. Reiner inspired us all and encouraged XSEDE scientists to become better communicators of our work by lowering the amount of jargon and in-depth details and focusing on connecting with our audiences by telling a stories that audiences can relate to.

All and all, it was  a great conference, with the opportunity to interact with our XSEDE partners, users, and each other.  We’re already looking forward to doing it again next year in San Diego!

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We recently had the opportunity to attend the International Science and Engineering Fair sponsored by Intel here in Pittsburgh.  There is one word I can think of to describe the fair: Awesome.

Aerial view of the science fair projects

There were over 1,500 high school students from all over the world, presenting their science and engineering projects for a chance to win a portion of the $3 Million in prizes.  These projects weren’t just your typical erupting volcano that we’re all familiar with – these projects were hard core, and these kids are going places.  Here are a couple project titles just to give you an idea:

  • - Optimization of Graphene Sheets as Electrode Materials for Dye-Sensitized Solar Cells Rahul Kumar age 17 from Fort Washington, PA
  • - Mitigating the Effects of the Morphine Signaling System: A Novel Treatment for Diabetes Cheng Yu age 18 from Commack, NY
  • - The Effect of Water Location on Salinity Based Upon Index of Refraction Jessica Lee Williams age 16 Ocean Springs, MI
  • - Electricity-Independent, Life-Saving High-Rise Building Emergency Evacuator Andriy Sytnyk age 16 Ukraine.
  • - Building Bridges with Water: The Floating Water Bridge Carolin Charlotte Lachner age 18 Germany

In addition to being able to pursue the 1,500 projects on the exhibit floor, the fair had an expo hall that featured corporations, universities and of course PSC.

students at our expo booth

Cheryl Begandy, Dave Graham, Tom Maiden and I got to talk to a lot of students about supercomputing. It was a lot of fun to see the kids’ faces when they realized what these big power house machines can do.

In addition to participating in the expo, we also had a couple of staffers serve as judges for the fair. Derek Simmel served as a Grand Awards judge in the Environmental Sciences category. Nathan Stone was a Co-Chair of the Physics Grand Award. Nathan comments on his experience as Co-Chair:

“These students cover virtually all physics topics from quantum mechanics to table-top neutron beam generators and astrophysics at the graduate level, it’s some pretty deep water to swim in.”

View from the convention center

All and all it was a great event to participate in.  We had the opportunity to engage with a lot of students who are really excited about science and engineering, and we’re looking forward to working with some of these students in the future as they move on to bigger and better things!

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