1.084/20.106  Systems Microbiology

Grades for all psets posted

Hi everyone,

I've posted grades and comments for all the psets this semester. Let me know if you can't see your grades or if you have any questions on the homeworks and/or grading.

Good luck with your proposals, looking forward to seeing what y'all come up with! Feel free to reach out to me via email if you want to discuss your proposals next week.

Have a great weekend,
Claire

Announced on 05 December 2015  8:52  p.m. by Claire Duvallet

Material from today's Bayesian thinking exercise

Hey everyone, see message below from Eric re: today's class:

-----------

I've updated the Bayesian thinking materials on the Github repository that I've used for this module on HIV (https://github.com/ericmjl/systems-microbiology-hiv).

Two additional packages are needed to run the PyMC3 example:
- theano
- pymc3

Installation instructions are available on the README file.

This is for class interest only, not as a homework/p-set.

Cheers,
Eric

Announced on 01 December 2015  5:39  p.m. by Claire Duvallet

Download BEAST for today's class + lecture slides available

Hi everyone,

Please remember to download BEAST 1.8.2 for today's lecture (link here: http://beast.bio.ed.ac.uk/downloads)

Also, I've uploaded today's lecture slides to the "Lecture Slides" folder on Stellar if you want to download them ahead of class.

Claire

Announced on 01 December 2015  1:06  p.m. by Claire Duvallet

Follow up from today's lecture + HW8

Hi everyone,

Hope you enjoyed lecture today, thanks again to Eric, Wendy, and Islam for putting it together - can't wait for the next couple of classes! A few follow up points that we mentioned at the end of class:

1. Python 3:
The README.md has been updated with instructions on how to get a new conda environment going with Python 3.5 inside it. Please re-download the Github repository and run those instructions (https://github.com/ericmjl/systems-microbiology-hiv). If you encounter problems, contact Eric (ericmjl@mit.edu). He can debug with you via email/Google Hangout. Like always, the more information you send him about your bug, the more helpful his response will be!

2. Work left from this lecture.
This is highly recommended to do, but nonetheless optional. Run through today's notebooks on your own (Lecture - HIV Data Exploration (Student).ipynb). You are encouraged to use the Student version, but you can still peek at the Instructor version to get a hint on what to do. Right at the bottom of the notebook, you will produce a FASTA file and a CSV file that will be used for the next lecture. Email your FASTA file and CSV file to Eric as soon as you're done, so that we know you've had no problems with the notebooks.

3. Notes on the P-set.
The pset is in the Github repository you downloaded (Problem Set.ipynb). All of the code that you need to write for the p-set is present inside the lecture notebooks, so we're mostly evaluating that you understand how all the pieces fit together (rather than asking you to write things from scratch). Write your answers inside the Jupyter notebook, no need to write them on a separate document. Email the p-set to me (duvallet@mit.edu) when done. Due date is Thursday, 3 December 2015, to give you enough time, knowing that you have your proposal to write. Eric is available for contact up till 1 December 2015 if there are clarification questions about the problem set, so contact him early if you see things that are unclear. I am also happy to hold office hours by appointment the week after Thanksgiving - just let me know what day is best for us to meet and we'll find a time that works for both of us. I'm happy to go over both the pset and the material we covered in class today, since it was a bit of a whirlwind!

I hope you had fun today, and have a great Thanksgiving!

Claire

Announced on 24 November 2015  7:11  p.m. by Claire Duvallet

OH today + action items for tomorrow's lecture

Hi everyone,

Hope problem set 7 is going well. Let me know if you encounter any problems with it, I'll be free for OH today 3:30-5 pm. If you plan to come by please send me an email first so we can coordinate where to meet in NE47. If you're not free today, feel free to email me and we'll see if we can find some time to meet tomorrow.

We'll be having another guest lecture tomorrow. Please bring your (fully charged) laptops to class, as we'll be asking you to follow along with some code. Also, you will need to install the joblib and python-Levenshtein packages for all of the code to work. If you are using a Mac/UNIX terminal, you should be able to install both by typing "pip install name_of_package".

If you are using windows, you can install joblib by typing "conda install joblib" into either cygwin or Anaconda shell prompt terminals. To install python-Levenshtein, open your Anaconda shell prompt and type "easy_install python-Levenshtein". If you get an error message that Microsoft Visual C++ 9.0 is required, go to http://aka.ms/vcpython27 to install it and then try again.

There are other dependencies used in this code and your pset, but if you installed the Anaconda distribution at the beginning of the semester and biopython last week, you should be all set after installing joblib and python-Levenshtein.

The lecture materials for tomorrow are here: https://github.com/ericmjl/systems-microbiology-hiv. Please download this repository as a zip file and run the check_env.py script before class tomorrow, to make sure you're all set up. There are more instructions in the README.md file in the repository. For Windows users, another way to access the notebook (if typing jupyter notebook doesn't work) is to go to your start menu and start iPython Notebook. This will open your browser and let you navigate to your unzipped directory containing these notebooks.

Let me know if you have any questions,
Claire

Announced on 23 November 2015  1:55  p.m. by Claire Duvallet