Thursday, June 14, 2012

CSLS Yearly Retreat

One of our local sources of excellence is the undergraduate program in "Computer Science and Computational Biology" which is often nicknamed CSLS. This elite program accepts relatively few students (~20/year) with very high entry grades. The students study both Computer Science and Life Sciences as well as specialized courses. To meet these requirements the program has a very high courseload.

Overcoming the challenges of such a program is often dependent on team spirit. Classes that formed a supporting social group usually had better success and the students felt they learned more and were happier. To help form such interactions we employ various activities, including specialized classes and study sessions for this group. One of the most important activities is the yearly retreat.

In the retreat, which takes place toward the end of the academic term, we take students in all stages of the program together with the teachers and TAs of the program.

The location of the retreat is Hof Dor, a beautiful beach that borders a large nature reserve along on of the most unique shorelines in Israel.

Although we spent two days next to the beach, most of the day was in the lecture hall.

The packed program had talks by senior year students who presented their final project. These projects involve working with researchers at the Hebrew University on a range of topics.

The talks in the retreat serve as a milestone in the project, as they provide a chance to present the research question, methods and results to a supportive audience. For the younger students these talk open a window to current research questions and how computational analysis plays a role in a range of biological studies.

Many credits go to Naomi for mentoring the projects throughout the year and working with the students on the presentations.

In addition we had a a keynote talk by Nathalie Balaban on non-genetic variability in bacteria and it's evolutionary importance.

However, sitting in a hot room listing to talks can be tiring.

To fight the sleepiness, Naomi arranged for an impromptu streach session, and later a musical interlude.

In spite of the heat, many of the talks inspired interesting discussions.

To top things off we ended the meeting with a guided trip in the nature reserve.

Alon and me took advantage of the flat sea to do two quick dives (one in the evening and the other early in the morning) at the local beach.

Tuesday, June 12, 2012

Dan David Prize

The last two days were a celebration of the Dan David Prize. This is a prize donated by the late Dan David and hosted by Tel Aviv university. The main prize is very large, and every year is given in three areas representing the past, the present and the future. This year the future looking subject was "genome research" an area close to us. The winners were David Botstein, Eric Lander, and Craig Venter. All three were main players in the sequencing of the human genome, but did much more before and after this milestone.

From the left: Craig Venter, Eric Lander, David Botstein, TAU rector, Lady Gilbert, Smadar Fisher.

One of the nice aspects of the Dan David prize, is that each winner "donates" 10% of the prize to fellowships that are awarded to graduate students in the same field. Both Moran and Michal were selected as recipients of the graduare student prize work in the genomre research catagory. In total 5 Tel Aviv students and 5 international students were awarded. Thus out of the 5 non-TAU winners, two were related to our group.

Michal getting a hug from Eric

Moran posing for a formal photo

To add to the story, Moran and Michal were of the same year in undergradute studies here in our Computational Biology program, and are good friends. Moran continued to do her MSc with me, while Michal did her MSc at the Weizmann. Moran continued to her PhD studies with me, but during the course of a collaboration with Aviv Regev at the Broad, she became co-advised by Aviv. More or less at the same time Michal started her PhD studies in MIT, and after a year of rotations elected to study with Aviv. I became involved with Michal's research through a collaboration. Since then Michal spent several long visits in our group and is now an integrated part of our lab.

The two prize winners

Picture with the two advisors 

And so, both Moran and Michal were awarded the Dan David graduate prize by Eric Lander the head of the Broad Institute, where they both do research.

Thursday, June 7, 2012

IBS 2012

Today I was hosting the IBS 2012 meeting. Officially the "14th Israeli Bioinformatic Symposium" which is the annual meeting of the "Israeli Society for Bioinformatics and Computational Biology" of which I was the president until few hours ago.

The meeting brings together researchers in Bioinformatics, Computational Biology and Systems Biology from all the universities in Israel. Traditionally we have an invited speaker from abroad, and this year it was Manolis Kellis from MIT.

The last few weeks were hectic with setting up the website for registration and poster abstract submissions, selecting caterer, and such. Late last week we decided to order buses to transport people to/from the meeting from all the other major academic universities. This meant that we had to set up sign-up forms and make sure all the people made it to the bus. 

Yesterday, I was away, but my local help (Dikla and Cecile) made the preliminary arrangements. When I showed up at 7am, the outer area was already with poster stands. Since we had more than submitted posters, we needed quite a few stands.

Not long afterwards, the florist showed with a nice flower arrangement. I was working with the A/V people to set up the stage properly. The large Wise auditorium was ready for action.

Toward 8:30 we had our registration desk with name tags set up and waiting for people to arrive. We had large signs and posters up and ready. The first wave of attendees were on the bus from Rehovot. 

After welcome remarks by our Vice President, we had the pleasure of hearing Manolis. He did a great job of showing why the new flood of data can make a difference in personalized medicine and how this is going to come about.

Overall we had more than 350 registrations. Not everyone who registered showed up, but we also had quite a few walk-in. I think it is safe to say we had more than 300 attendees, maybe closer to 350. (We ordered food for 350 and it was all finished).

The closing ceremony involved the "Best Poster Awards" that were selected by a committee of faculty members (I was not involved). It was a nice surprise to find out that our very own Assaf was one of the poster winners.

By 5:30pm, the meeting was over. I helped wrap things up, and thenI headed to my office to find a water leak :-(

Tuesday, June 5, 2012

Leaky sprinklers

Some of our readers might think that once we finished the renovations our infrastructure issues were solved. In my view we don't pass a week without some sort of problems or issues to deal with.

This week it was the sprinkler system. Some explanation is needed.

Few years ago one of the chemistry building went up in flames (as chemistry buildings often do). As a result, the building had to be totally renovated. Luckily the damages were mostly (or only) financial. After this unfortunate event the firm that provide insurance for the university raised the premium as long as the university does not put in fire prevention devices. This resulted in a long process in which new sprinkler systems were added to existing buildings.

Our turn was up earlier this year. We went through a series of meeting where were told of the importance of this move, and how the best choices have been made to minimize the chances of a fire (on the one hand) and accidental dosing (on the other). We were told that the firm that installs these sprinklers meets the highest standards for quality and cleanliness and would be "virtually unnoticed" when they worked.  I was one of a group of researchers who expressed worries about our delicate equipment getting damaged by the installation works or getting water damaged post-installation. As such we were further soothed by responsible administrators that there will be tight supervision of the works and the "acceptance tests".

The following months were rather annoying. The worker closed part of our parking lot and used it for cutting pipes. They had to drill halls through the concrete structure along the hallways and between hallways and labs to traverse the whole building. When they worked inside the lab we had to remove all items from benches and shelves and cover these to protect everything from the dust (as they needed to make large holes in concrete). Luckily for us, the work in the robot room was less painful, as they found pre-made holes they can use and did not need to drill new ones.

Few weeks ago the system became operational. Although it was supposedly checked for leaks, the first day we had a leakage in our corridor. When they came to fix it, they did not drain the water properly and caused a major flood along part of the corridor (luckily further out from our lab).

Today, I came in and noticed that the floor in Cecile's office (the outer room to my office) is wet. Initially I took it to be remains of the cleanup earlier in the day. But then I noticed that the wall was also wet. A quick examination showed that the slow, but steady, leak was from the ceiling. Opening the ceiling tiles, I immediately saw the source --- a junction in the sprinkler system. 

Calling the maintenance department, I got a response relatively fast. It turned out they increased the water pressure this week, and therefor they were discovering junctions that were not properly sealed. To fix the problem, the fellow banged on the junction with a hammer and claimed that this puts the o-ring into place. I was not convinced, but after waiting an hour it seemed that the leaking stopped.

And so, we all wasted an hour and half during one of the busiest day of the recent months. I should be thankful that this did not occur above any sensitive equipment.

PS. Two days later, I returned to the office (I was out due to conferences and such) to find the whole area wet. Seems that the leak returned. This was late afternoon and I had to call an emergency maintenance person. He closed the water to the whole corridor and depressurized the system.