Technion, Israel Institute of Technology
Faculty of Biology
Computational Approaches for Life Scientists 134141
Spring Semester 2016


Amir Rubinstein, li.ca.uat|rrima#liame
Office hours: before or after class - please coordinate by email.

Teaching assistant:

Gur Hevroni, li.ca.noinhcet.supmac|inorveh#liame
Office hours: please coordinate by email.

Course syllabus:

Detailed description in English


Final report submission date

Hello all,

A reminder that the date is August 4th.

Also, I uploaded a short survey to moodle, which I ask you to fill.

the feedback is very important for me.

Good luck all,


(16 Jul 2016 14:23)

Cell quantification competition winner

The image we used for labeling demonstration in class was taken from this website: http://www.broadinstitute.org/bbbc/image_sets.html. It contains many image sets that can be used to test image processing algorithms.

The specific image we used is from the data set called BBBC004 (http://www.broadinstitute.org/bbbc/BBBC004), which contains synthetic images. There are several sets, and I chose the one with overlap probability = 0, the file named 1GRAY.tif.

Since this is a synthetically generated image, the "ground truth" mentioned on the site is accurate: exactly 300 cells.


So, we have a winner in our competition - well done Omer!

I remind you that next week there is no class, Tuesday is acting as a Thursday.


(18 May 2016 07:22)


is online.

(10 May 2016 21:22)

HW3 bonus - betweenness

In Q1 you are asked to implement max_betweenness, by a simple loop that calls find_betweenness for every node in the graph.

Students' questions raised my awareness to the fact that this is a highly inefficient solution: the same computations are done again and again, when Dijkstra's algorithm is called for every source node many times. Such a solution, as you figured out, takes hours to terminate (it tool some 10 hours for some students).

A more efficient solution, that calls Dijkstra only once for every node takes on my computer less than a minute (!). You will get 5 bonus points for implementing such a solution.


(04 May 2016 07:36)

HW3 is online

It's about graphs and discrete simulation.

See you next week,

(24 Apr 2016 16:42)

HW2 is online

Good luck,
the course staff

(06 Apr 2016 19:52)

HW 1 is online

Hello all,

HW1 is online, due in 2 weeks.

We opened a forum for Q&A on our website. You are welcome to ask and reply to your friends, and we will also visit the forum occasionally.
I recommend starting to work on the HW soon, because you may (and probably will) get stuck here and there.

Have a fruitful work,
The course staff

(22 Mar 2016 19:16)

Following the first meeting

שלום לכולם,

במפגש הראשון היום הצגתי את מטרות הקורס ואופיו, וכן את הנושאים שייכללו בו, ולאחר מכן התחלנו להכיר את שפת התכנות פייתון.

נמשיך בכך גם במפגש הבא. לקראתו, אנא עיברו על מה שעשינו היום, פיתרו את התרגיל משקף 22 (מצב צבירה ו"זכוכיות" של חומר), וכן את השאלות בדף התרגילים exercise.pdf (אלו בעיקר שאלות "חימום", שנועדו "לידד" אתכם עם פייתון). ככל שתשקיעו יותר כרגע בהיכרות עם השפה, כך יהיה לכם קל יותר בהמשך.

בנוסף, הקישורים לתרגילי הבית מהשנה שעברה, שלא עבדו, תוקנו.


צוות הקורס

Dear all,

In our first meeting today I presented the course goals and spirit, as well as the topics we will learn, and then we started our acquaintance with Python.

We will continue with this next week. For the next meeting, please review what we did today, solve the question from slide 22 (state of matter and glassy state), and the questions from the exercise.pdf sheet (these are mostly trivial questions, which aim at familiarizing you with Python). The more you put an effort now, the easier it will be later.

The links for last year's HW are now fixed.

The course staff

(15 Mar 2016 19:44)

ברוכים הבאים ל"גישות חישוביות במדעי החיים"

שלום לכולם,

ביום שלישי הקרוב יתקיים השיעור הראשון בקורס.
אתר הקורס נמצא ב- http://ca4ls.wikidot.com
שם תוכלו למצוא פרטים על מבנה הקורס ותוכנו, הרכב הציון וכו', וכן את חומר השיעור הראשון.

מכיוון שזהו אינו קורס סטנדרטי בפקולטה לביולוגיה מבחינת תוכנו ואופיו, אני מציע לשוטט באתר, וכן בחומר של הסמסטר הקודם (הרצאות: http://ca4ls.wikidot.com/material-2015, תרגילי בית: http://ca4ls.wikidot.com/hw-2015), כדי להתרשם ולראות אם אכן הקורס עונה על ציפיותכם. בנוסף, בשיעור הראשון אציג את הקורס במפורט. אתם מוזמנים גם לשאול אותי במייל (מופיע באתר) אם יש לכם התלבטויות. בקורס זה הסטודנטים מצופים להופיע לשיעורים, וחלק מהציון (10%) ניתן על בסיס זה.

באתר מופיעות גם הנחיות להתקנת Python IDLE - התוכנה איתה נעבוד הסמסטר ובה נכתוב תוכניות בשפת התכנות פייתון, ונדגים נושאים שונים ממדעי המחשב. כדאי להתקין את התוכנה לפני השיעור הראשון, כדי שמי שנתקלו בקשיים יוכלו לבקש עזרה.

צוות הקורס

Dear students,

Our first meeting is this coming Tuesday.
The course url is at http://ca4ls.wikidot.com, where you can find details about the structure and content of the course, grading, as well as the material for the first meeting.

Since this is not a standard biology course, I recommend wandering around on the website, as well as the previous semester's material (lectures: http://ca4ls.wikidot.com/material-2015, HW: http://ca4ls.wikidot.com/hw-2015), to get an impression and see if the course indeed matches your expectations.
On the first meeting I will also present the course in detail. You are welcome to write to me if you have questions.
In this course students are expected to show up for the meetings, and 10% of the grade is based on that.

The software we will use is Python IDLE, with which we will write Python programs to demonstrate topics from computer science. You can find installation instructions on the website, and it is recommended to install it before the first class.

The course staff

(10 Mar 2016 16:04)

Q&A Forum

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