A wet surprise

Seems like our building does not like holidays. If you recall, during Purim there was a big water leakage in the peer next to our lab. This passover as I came to visit the lab the security people asked me to watch out of the puddles. What? turns out there is a overflow in one of the bathrooms and it leaked through several levels of the building to the base level through which I came in.

The bathroom at our floor didn't look that inviting.

This morning the place was cleaned up without any signs of the catastrophe....

Visitor in the Lab

Today was the annual Israeli Bioinformatics Symposium, held by the Israeli Society for Bioinformatics and Computational Biology of which I happen to be the President. Our keynote speaker this year was Trey Ideker, and I hosted him on Monday for a sightseeing tour.

My student Moran joined us a a tour guide of the Old City of Jerusalem, which she knews quite well, and left me to document the visit. Few pictures to get your appetite for a visit here.

The Holy Sepulchre Church Jerusalem

Tasting some authentic humus  at Lina

Searching for gifts

From there Trey and I continued to the city of Caeseria, an old port city that was built (and destroyed and rebuilt) from the Roman time until the 14th century and now is an archaeological park.

Hot Water? Story of a red pipe

As the work progresses various surprises pop up. As I reported before, we had the water pipes installed all along the lab.

A very prominent pipe is the thick red one. This is the hot water pipe that runs along our lab from the peer on the one end of the lab and into the next one. It is thick because it is covered by insulation sleeves.

In the middle of the room there is a branch point where a branch goes down below the floor and out the other side of the room to connect to where we will have a sink.

Last week there was a site visit by the maintenance people. They pointed out that although the building has a hot water system (i.e., a dedicated set of pipes through all the labs), there is no supply of hot water, and in fact it will probably will never be supplied (I didn't get into the details of why).

So it turns out that this nice pipe is for naught, and we need to install electric water heating system in this room (and the other ones) for local supply of water.

Windows, doors, and tubes (a mid-passover report)

The last week or so I was on the road and did not get to see the building progress. On the few calls to the lab I heard in the background terrible noise. Turns out we finally got an electricity constructor and his workers were cutting tunnels to pass electricity wires in the walls.

Today I finally managed to get to see what this was all about.

The way the electricity layout is planned, we have a main board next to the door (the alcove that was built earlier on) from which electricity and communication cables will go up above the decorative ceiling, run along wireframe shelves, that will be hanged from these constructions

Then the cables have to reach the main service duct that will run just below window height (both below the windows and along the side walls). To reach that duct, the cables have to be routed through the walls, and the workers excavated wide passageways and prepared tubes, one per cable.

 

I am mystified why they cannot be routed through a normal duct (close to the windows), but I am not an electricity engineer.

The workers has started to seal off the tubes in cement and make them part of the wall.

Oh, and the new windows have been installed, except the ones on both ends that have to be build to fit. And we got a new door frame for the entry doorway (metal instead of wood, yay!).

On the road: Cold Spring Harbor (+Boston)

Devout followers of the Blog have probably noted the lack of updates the last week or so. I spent this time traveling. The goal of the trip was to attend the "Systems Biology: Global Regulation of Gene Expression" meeting at Cold Spring Harbor Labs (CSHL). This is one of the best meetings in the field, and I try to attend it when possible. For the last few years it has been scheduled for the week before passover, which meant busy flight schedule.

I started with a stop over in Boston. I landed on a crisp sunny day.

Ollie Rando (AKA "The Dude") a close collaborator and friend picked me up and took me to "The Barking Crab", one of the favorite waterfront places in town, for an afternoon light meal and scientific discussions. Bas van Steensel arrived a bit later (on a flight from Amsterdam) and joined us.

The next morning I took the train to Worcester and visited Ollie's lab. Heard a nice talk by Bas, and gave an informal talk about our lab in Ollie's group meeting. I had a good meeting with Marian Walhout, who uses the Singer RoToR for one-hybrid and two-hybrid screens in her lab. They are very happy with the RoTor and do not have the same issues we have.

The following day I visited Aviv Regev, another close collaborator and friend at the Broad Institute. It was nice to meet old friends in her group, and we also had productive discussions on various on going collaboration. Aviv and me then traveled together to CSHL for the meeting.

It was nice to meet many researchers I know, including ex-students Tommy Kaplan, Gill Bejerano, and Dana Pe'er. In addition I ended spending time with Arend Sidow, who I didn't see for quite a while. I won't list all the people I met, as the list would be long (and exhausting), but it suffices to note that I seem to know many of the attendees, which is a clear sign that I have been attending these meetings for a while (maybe too long?).

I shared a room in a wooden cabin with Tommy.  The room itself is very basic, and the cabin heating was either full blast or non-existent (so we alternated between severe heat shock to a mild chill). Moreover, our cabin was located in the furthest locaiton from the main meeting hall on the top of a hill, which meant that going there was a somewhat of a treck. However, by the nature of the meeting, one spends most of the time at lecture hall or in the pub (which is the main interaction hub).

On the last day of the meeting I learned to my surprise that my flight home is from Newark and not JFK as I thought. So I canceled the shuttle service I ordered to JFK, and instead took the train to Penn Station and then to Newark. I had a bit of time to get outside and get a sense of the feel of the big city.

We took off from Newark at sunset which left an impression.

Some lab updates

So its been a while since I had updates from the lab. The main reason is that things are going slow and I don't spend that much time there.

Nonetheless, few updates and some images. We finally got our very own ice-buckets (for some reason our lab-ware supplier had these in backorder for two months).

We are also testing a PCR machine. We got an offer to buy a machine from a reletatively unknown vendor that has good specs. To get a sense for it, we got a demo machine installed in our lab.

One of the nice features of this PCR machine is that has a detachable block, and so it can be either a 96-well block (for a full plate PCR or many reactions) or two 48-well blocks, allowing to run two reactions in parallel.

Next week we will get another machine for a demo, and then we will decide which one to keep.


As part of our work we often have to grow bacteria or yeast in colonies. When starting with very small amount of cells that can grow on the media, we often want to spread them on the plate. The common way of doing so is with a bunch of sterile beads. You pour some onto the agar

and then add the bateria dilluted in water (or liquid media)

and shake well.

After wards we discard the beads into a collection bottle for recycling, and move the plate to incubator for overnight growth.

Pipes, Windows, and Sky

Last week the renovation work slowed down a bit, but now we are starting to pick up the pace. We had a window contractor come in to install a window for demonstration

Eyal, our project manager, approved the window with some additional modifications, and so soon we will have the whole row of windows replaced.

Yesterday our new A/C and installation contractor started working. His worker replaced the temporary pipes with new ones.

Outside the hazy warm days were replaced by clear and windy ones. Walking today from the lab back to my CS office I saw the potential for impressive sky.

(The crane is the building site for the new engineering building that should be finished in about a year and half.)