Author Archives: Greg@WM

T-shirts will be mailed

If you do not get a T-shirt before you leave the course, be sure that Andrea Stephenson  <> 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: Mariam Ghochani – Statistical model in extracting protein associations

The anatomical distribution of multiple proteins within complex tissue is predicted to aid in the determination of musculodystrophy. The data from multiplexed proteomic imaging method of array tomography is a very rich data set that enables detection and characterization of each pixel with multiple numbers of markers. The tissue architecture of the samples and thus the inter relationship of multiple cells can be preserved and studied at resolutions that are higher than that of other conventional microscopy methods by a factor of 5-10. This essentially provides us with a rich high-dimensional dataset. Such dataset can be studied in order to characterize Changes in abundance, localization and distribution of single proteins. But also the pairwise relations from such dataset can be studied to characterize changes in the pairwise relationship of proteins in relation to the same complexes. The high dimensionality of this dataset will enable study of higher order and changes in the complex relationships of proteins as part of multi-partner ensembles as well as classification of compartments in terms of their associated heterogeneous protein markers. Having many markers per pixel will help to statistically increase the significance of classification of pairwise relationship, complex associations and classified compartments against sensitivity and specificity of recognition/detection. The underlying hypothesis for my model is that the false positive and false negative errors in the detection will not affect the pairwise and higher-order associations of proteins when analyzing/classifying with large number of markers and large distributions. For this the algorithm for modeling and simulation is as following:

1. Generate rich datasets.

2. Simulate different levels of noise in the dataset.

3. Confirm that with different levels of false positives and false negatives, the protein associations can still be extracted from dataset as long as the number of classifier and dataset is increased.

4. Prediction of the model: the sensitivity and robustness of the statistical model in extracting pairwise and higher order protein associations.

In this project, I attempted to develop a model for the proposed model-based statistical analysis that encompasses the alternate asymmetry of binding of DHPR to RyR in skeletal muscle.

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

Introducing Reka Albert

[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

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.