Category Archives: Uncategorized

T-shirts will be mailed

If you do not get a T-shirt before you leave the course, be sure that Andrea Stephenson  <stephens@cshl.edu> has your correct mailing address as soon as possible, because in that case she will mail your shirt to you.  The default address is the one you used when you applied for the course and/or registered for housing.

Final Project: Qingyang Ding – How dynamics of transcription factor control gene expression

   Inspired by the idea that signaling dynamics can encode cellular information, I built a set of toy models of gene transcription controlled by different dynamics of transcription factor (that is oscillatory or sustained) to investigate how different promoter response to those dynamic inputs. Many software I learned from the course are involved in the implement and analysis of the models, including XPP, Copasi, and CRNT. I tried to understand the feature of promoter with the help of bifurcation diagram, and also optimize a designed variable of the model to qualitatively fit the experimental results. While plain promoter (with only mass action rules) didn’t discriminate oscillatory and sustained input much, promoters with feed forward loop and positive self-feed-forward loop shows that the average level of oscillatory response is much lower than that of sustained response. What’s more, the feed forward loops also contribute to a significant delay in terms of gene expression. The methods and workflow can be used in building and analyze more transcription models with diverse regulatory mechanisms.

Remember to return library books

Hi guys,

I am listing the names we have on the record for the books that are out. One book has no name on the record. Please return the books as soon as possible or let me (Sajiya) know if you find the missing book. Thank you.

Nazilla: Random walks in biology (c.1), Learning Matlab, A guide to XPPAUT, Computational cell biology

Mariam: Calcium signaling, Nonlinear dynamics and chaos

Wei: A guide to XPPAUT, Mathematical foundation of neuroscience, Physical biology of the cell.

Niamh: Computational cell biology, A primer of mathematical models in biology.

Sepideh: Stability, instability and chaos; Systems modeling in cellular biology.

Illyce: Biochemical oscillations and cellular rhythms.

Bharat: Elements of applied bifurcation theory, Stochastic modeling for systems biology.

[unknown]: Computational modeling of gene regulatory networks – a primer.

Introducing Reka Albert

http://users.phys.psu.edu/~ralbert/

[Reka will be speaking Wednesday afternoon and Thursday MORNING, as opposed to afternoon, so as to avoid conflicting with the plate race.]

Introducing Martin Feinberg

http://www.crnt.osu.edu/people/feinberg.14

Sailing is still “on” … meet at front of Grace Auditorium at 12:30

Even though there is a chance of rain, the Waterfront center is loathe to reschedule our trip; they say there are “no guarantees” if we try to push it back.  So we are going to get in the vans and go to the Waterfront.  If it is looking like no fun at all, we can drive back to Huntington and explore a bit.

Image

The CSHL CCB 2013 Course Photo!

IMG_9506_C_COMP

Photographs?!

I see some photos have been posted on the ftp server.  Keep them coming!

The people outside and in the small room…

The people outside are CSHL scientists and staff; there is a happy hour every Friday.   Maintain good relations, but the main classroom is off limits (because of all the computer equipment).

If the children come into the main room again, please remind them (firmly) that tonight they can play in the small room, but our main classroom is “adult swim.”   If you need a book or to print, feel free to do so, but shut the room to the small door when done.

Video

2012 CCB Plate Race – Part 2