6.047/6.878  Computational Biology

Presentations + Course Feedback

Hey everybody,

A reminder that the presentations of your final project will be held tomorrow in the lecture period (from 1pm to 2:30pm in 32-141) as well as in 32-D463 from 2:30pm to 5:15pm. The schedule of groups to present can be found here; please let me know as soon as possible if you won't be able to present in your assigned slot.

Please e-mail me your presentation as a PDF or upload it to Stellar by 12:30pm tomorrow. We will be running the presentations off of my laptop, so you don't need to bring your own. Be sure to keep your presentation to under 6 minutes in length, and be prepared for a 2-3 minute question period afterwards.

With the end of the semester in sight, it has come time for you to submit your final assignment of the class: end-of-term evaluations! Manolis and I would really appreciate it if you could follow this link and be as honest as possible in reviewing our presentation of the course this year. Thank you all for taking 6.047/6.878, good luck in the exams for your other classes, and have a happy holiday season!

Announced on 09 December 2015  5:10  p.m. by Michal Radoslaw Grzadkowski

Pointers on Project Report and Presentation

Hey everybody,

Here are a few tips as to what I'm expecting from your project report and presentation:

• Project reports are due any time on Sunday, December 6th. Project presentations are due by 1pm on Thursday, December 10th. I will generally be far less lenient on late submissions for the project, so if you need an extension, be prepared to give me a good reason why you need one.
• Your report should be structured into sections: 1) Background, 2) Methods, 3) Results, 4) Conclusions, 5) References. Methods and Results can be interwoven if you'd rather present your aims in order.
• Project reports should be between 6 and 12 pages in length. However, these are not fixed limits, as the length of your report will depend on your format, number of figures, etc. As a general rule, you should make your report long enough to show that you put significant effort into your research direction, but not so long as to bore me when I'm reading it. Focus on clarity and conciseness in your report, rather than an exhaustive presentation of everything you did for the project. I am not picky as to the format you use, put use good judgment in making your report easy to read.
• Presentations should be no longer than 6 minutes in length. Be prepared for a question session of two minutes after your presentation.
• Submit both your report and your presentation as a PDF to the Stellar website. Late submissions must be e-mailed to me personally.

A reminder that I'll be available in 36-112 today from 3pm to 4pm if you want to talk to me about your report or presentation!

Announced on 04 December 2015  11:38  a.m. by Michal Radoslaw Grzadkowski

Office Hours, Quizzes Handed Back, Pset Clarification

Hey everybody,

Office hours this week will be held in the D5 lounge on Wednesday from 4pm to 5pm and on Thursday from 3pm to 4pm. In lieu of the usual recitation session, I will instead be available in 36-112 on Friday from 3pm to 4pm to give tips on project write-ups and presentations.

The quizzes will be handed back in class tomorrow. You can also pick up your quiz at office hours. I have posted the grade distribution histogram to the Stellar course website under the Quiz Preparation Materials folder. The overall mean/sd for the class was 67/13, and 64/13,71/11 for the undergrad and grad versions of the class respectively.

A clarification for the fifth problem set: you only have to do Parts 1 through 3 on the website given - Part 4 is not required.

Announced on 01 December 2015  12:06  a.m. by Michal Radoslaw Grzadkowski

Pset 5 + Quiz Update

Hey everybody,

The fifth problem set has been posted on Stellar and is due Thursday, December 3rd, at 8pm. Note that this pset is only half as long as the usual pset and thus carries only half the weight.

The study guide for the quiz tomorrow lists genome assembly as one of the topics to be covered. However, since we didn't have a chance to cover it this semester you are not responsible for genome assembly for the quiz.

A reminder that I will be holding office hours today from 4pm to 6pm in the D5 lounge. I plan on covering the Burrows-Wheeler Transform and suffix arrays if enough people show up, but if you have another topic you would like me to go over, feel free to give me a heads up!

Announced on 23 November 2015  10:37  a.m. by Michal Radoslaw Grzadkowski

Review Session Update + Pset 4 Grades

Hey everybody,

Based on the results of our poll, the following topics will be reviewed (in this order) during tomorrow's recitation:

1. Multivariate HMMs for characterizing chromatin states
2. Phylogenetics (tree-building and Robinson-Foulds)
3. Latent Dirichlet Allocation
4. Bayesian networks
5. Coalescent Theory
6. String search (Burrows-Wheeler Transform and Induced Sorting)

I don't expect that I'll be able to cover all of these topics in the hour, and so we will be spilling over into office hours - you can come for whatever portion of the session you feel is necessary. I will also be holding office hours on Monday from 4pm to 6pm in the D5 lounge if there are any other topics you would like me to go over.

The fourth problem set has been marked and the grades have been uploaded to Stellar - note that they have been revised upward since last night. The grade distribution for Pset 4 has also been added to Stellar.

Don't forget that your midcourse project reports are due any time on Wednesday as a single PDF document for your team, uploaded to Stellar. I will be providing a project grade projection for you by the end of the week based on the work you've done so far, i.e. your proposal, review panel rebuttal, and midcourse report.

Announced on 19 November 2015  4:42  p.m. by Michal Radoslaw Grzadkowski