Category Archives: Announcements, Lectures & Exercises

Posting Your Final Project Presentations

There are two (2) different steps to posting your final project presentations.

1. Write an ~200 work abstract that summarizes your project.  You can use the text of your project proposal post as a starting point, but don’t edit the project proposal, make a new post.

Use the format “Final Project: NAME1 NAME2 – PROJECT TITLE” as the title of the post, e.g.,

Final Project: Greg Smith – SimPlateRace v1.0 🙂

Don’t take more than 3o minutes to write your abstract.  It need not be comprehensive, but please write it well enough that I can copy and paste it into the annual report that goes to the NSF program officers.

2. Upload your final project presentation slides (e.g., .ppt and/or .pdf) to the FTP server (in the folder FinalProjectPresentations).  Make the title of the file informative (e.g., the first and last names of the presenters).   You can upload changes until the last second, but get a draft on the FTP server by midnight tonight.

Presentations are tomorrow after lunch.  Don’t stress too much.  Have fun!

Note: if anything you have done here makes it into a publication please mention the “2013 CSHL Computational Cell Biology Course” in the Acknowledgements section.  And send me an email with the paper attached!


SimPlateRace v1.0

SimPlateRaceSnapShotThe computational cell biology course has just completed a CSHL Plate Race simulator (beta version).  It is “closed source” for now (about 200 lines of hastily written matlab code), but we hope you will enjoy this example output (visualization of a simulated race) by following this YouTube link:

Comments and suggestions for v2.0 (Summer 2014) are welcome.

Introducing Jeff Hasty

Today’s Schedules Changes

Todays schedule has (again) been subtly tweaked:

Lecture from 9-12
Lecture/Exercises from 1:30-2:30
Plate Race 3:00-4:00 (near Delbruck, you can’t miss it)
Student projects 7:00-10:00

Student project meetings & updates

In the title of your student project post (and below), you will see that you have been assigned a project consultant.

Please meet with your consultant today or Wednesday. This is a good opportunity to make sure you are on track, obtain perspective on a model that you are developing, get help implementing a model in a particular software package, etc.


Investigation of Traveling Waves in the Belousov-Zhabotinskii (BZ) Reaction, Jasmin Imran Alsous, Megan Matthews

Noisy gene expression resulting from G-Quadruplexes – Bharat Ravi


Mathematical model of autophagy activation pathway – Eric Yang

The circadian rhythm and its robustness – Wai Shing Lee


Parameter optimisation for a model of AMPK-mediated survival signalling – Niamh Connolly

Post transcriptional regulation in metabolic transition in E.coli, Manon Morin, Sepideh Dolatshahi

Modeling cell cycle re-entry and differentiation – Tim van Mourik


Dynamics and transcription [Qingyang Ding]

Incoherente Feedforward loop for cell cycle reentry [Alicia Grande]


CGG RNA affects granule assembly, translation and calcium transients – Rene Norman

VE-cadherin dynamics – Nazila Daneshjou

Microtubules and Cdc42 dynamics – Illyce Suarez

To get plates – for plate race practice

The yeast genetics course is in Delbruck…we need a couple CCB students to stop by after dinner to grab plates.  They told me they will set out a stack for us.

Course Banquet Entree Choices – Post Your Choice as a Comment

There are three choices for the banquet entree:

  • Lobster
  • Steak
  • Vegetable and Tofu Napoleon

As soon as convenient, please make your choice and post it as a comment below.  Format:  NAME, [Lobster/Steak/Vegetable]

CSHL Tour is today @ 4:30 leaving from inside Grace Auditorium

Our our guide will be Zina.  She will give a campus tour today at 4:30PM. The group can meet in Grace Auditorium.

Enjoy the evening and Sunday…

… we start again at Monday 9am (rule-based modeling).

Due to the rain earlier the course picnic will be held in Blackford hall

Due to the rain earlier the course picnic will be held in Blackford hall.

Course Picnic ~ Saturday, August 3
Rain Plan: Blackford Hall
4:00pm – 5:00pm Bar & Raw Bar / 5:00pm – 7:00pm Bar & Buffet