Grades updated - clarification
Just to clarify - in the process of updating a small subset of grades, I uploaded the wrong file, and it made many other grades change. I then uploaded the correct file, with the final corrected grades.
So you might have seen 2 changes in the grade.
Students who know their grade should have change - should now see the final grade on the site. Students whose grades shouldn't be changed should see their old grade back on the site.
Sorry for the confusion.
Students who know their grades should change (after talking to the course staff) - please check them now on the site and let us know if there is any problem.
On Sunday we will send all the grades to UPGRADE.
The project grades and final grades were now uploaded to the site.
The grade was calculated as follows:
• 5% for every HW assignment (20% /4)
• 8% for research proposal (80% * 10%)
• 8% for meeting with supervisor (80% * 10%)
• 64% for poster presentation (80% * 80%)
Please find on the side under Course Material/ Final Projects a list of all groups with the numbers of your posters.
Posters with odd numbers will be presented on the first hour (12:30-13:30) and the posters with even numbers will be presented on the second hour (13:30-14:30).
Nevertheless, it is *mandatory* for all students to attend in the whole 2 hours of the poster session.
Poster day-THIS WEDNESDAY 21.3- Presentation instructions
Now that you have all submitted your posters it is time to get ourselves prepared for the presentations!
As you all know the poster day is on Wednesday 21.3 between 12:30 to 14:30 (Zohorei yom Daled)
in Taub (computer Science) Building room 337.
Please make sure to be there 10 minutes before it starts to find your posters and get organized!
It is mandatory that all students will be present during the entire time !!
Full instructions for the poster day and tips how to get prepared have been now uploaded to the website
under "Final Projects" .
If you have any specific questions please contact your supervisors.
We are all looking forwards to the exciting event.
See you all on Wedndesday
The course Staff
Poster submission - on site
The poster submission is now available on the site (HW/ Final projects - Poster submission).
We allow submission until Saturday night (17/3). No extensions will be granted!
Please submit posters in PDF format only. Make sure you created the poster in power point with 120cm X 90cm slide size (portrait orientation) and only then converted it to PDF.
No proofreading is done on the submitted posters, make sure you have no mistakes or typos.
Project and poster feedback
The deadline of the poster submission is in 10 days (16/3). Note that we will *not* be able to give any extensions as we need a few days to print all the poster for the poster day.
We would like to remind you that it is highly recommended to get feedback from your supervisor on the project and poster. We will not be able to give feedback after the submission due date, as in Sunday morning (18/3) all posters are sent for print.
Please plan ahead to write to or meet with your supervisor and give us time to return feedback and allow you to improve your project and poster.
Example posters + feedback on research proposals
We now published example posters (under "Course Material"), for you to view.
Each supervisor will send feedback to his/ her groups for the research proposals you submitted this upcoming Thursday via mail.
Good luck with the projects,
Submitting a project proposal- January 30th at midnight
We would like to remind you that this Tuesday January 30th is the deadline for submitting the one
page proposal of your project!.
As written in the instructions, given in class and posted on the website, the proposal should include:
-Title of the project (as decided with your supervisors)
-Main question (including a description of the question and background)
-General plans, including the data set and bioinformatics tools you are planning to use to answer the questions and the
*Each proposal should include the names and IDs of all members of the group.
*File name should be proposal_your initials_name of supervisor.PDF
Please submit the proposal via the website, under course assignment not later than midnight January 30th.
A reminder- The one page proposal consist 10% of the final project grade
and have a successful exam period!
The course staff
Guest seminar tomorrow in class 15:30-16:30 -Don't miss it
Tomorrow, at the first hour of class 15:30-16:30 we have a special guest seminar by Dr, Inbal Budowski-Tal.
Dr. Budowski-Tal works in a bioinformatics company , name BiomX.
BiomX, is a pharmaceutical startup that develops novel therapeutics to alleviate microbiome-related diseases.
The company develops computational platforms to harness microbiome data for drug discovery.
In the talk Inbal will describe the road the company made from a totally computational startup to the pharma industry,
and the computational tools they developed to discover meaningful insights that assist in developing drugs.
During the talk you will have time to ask questions about opportunities for Bioinformaticians in industry and hi-tech.
DO NOT MISS IT!!!
The course staff
Supervisors for the final projects + meetings on Monday
In the upcoming Monday (January 22nd) each group will meet with its supervisor for the final project.
Please find in the site a list of groups and supervisors, along with the meetings schedule and location. The file is under "Course Material/ Final Projects".
We would like to remind you that the meetings with the supervisor are *mandatory* for *all* group member, and you will be graded on it (10% of the final grade).
You should come with an initial research plan in mind - What is the research question? What is the data you will work on? What tools and methods you will use to answer the question?
You should also come with questions to the supervisor (if you have any), and you are welcome to consult with us - this is what the meetings are for. That being said, we *will not* help groups that did no initial planning on their own in advance.
The meetings will take place on Monday on the time of the tutorials and on the second hour of the lecture. Some of the meetings were scheduled after the lecture. If any of the groups who were scheduled to meet past the time of the lecture cannot attend, please contact your supervisor to schedule an alternative time.
In the first hour of the lecture on Monday you will have an invited lecture from a bioinformatician working in the industry. More details to come!
Have a nice weekend,
Tutorial today at 15:30
We would like to remind you that the tutorial today is at 15:30 instead of the lecture.
There will be no tutorials in the regular times.
Additional reception hour for projects + Change in tutorial hour next week
As some students could not attend the reception hour last week, I am setting another hour for questions.
It will be held on Monday, 14:30-15:30 at the auditorium at the Science Education Faculty.
Note that next week, there will be no tutorials at the regular time. The tutorial will take place at the first hour of the lecture (15:30-16:30) for both groups together.
There will be no lecture. We advise you to use this time to work on your projects.
Have a nice weekend,
FAQ for HW4 opened
Please find HW4 FAQ on the site.
Tutorial today- in the biology computer farm
|Hi all, this is a final reminder that the tutorial today will take place at the computer farm in the biology building at the regular tutorial times.|
The computer farm is opposite the biology auditorium on the second floor (1 floor under the main entrance).
The tutorial will be given by an expert in structural biology Dr. Akram Alian.
All material will be provided in class.
Don't miss it
The course staff
Reception hour for projects
As some of you asked for consultation regarding the projects, I'm setting up a reception hour on Thursday, January 11th.
It will take place on 12:00-13:00, at Emerson 3-7 (the seminar room at the 3rd floor).
We want to remind you that the tutorials tomorrow will take place in the computer farm at the Biology faculty.
You will have a hands-on tutorial on a program that allows molecular visualization of proteins. This is very relevant to many of the projects.
Note - there will be no material available for this tutorial later on the site.
The tutorial is relevant for English speakers as well.
Have a nice week,
Registration for final project
In order to register for a project, please use the following form:
Only one registration per group is needed.
Deadline for registration is January 16th.
list of proposed projects for final assignment 2018
A list of suggested topics for final project has now been uploaded under "Final Projects".
Remember the final date for choosing a project is 16.1.18.
All instructions and key dates related to the projects have also been uploaded.
The course Staff
The forth and final HW assignment was published.
Due date is January 9th.
FAQ for HW3 was published
FAQ for HW3 was published. Please be sure to check all updates in the FAQ before submission.
Our special schedule for tomorrow 11.12.17
As you all remember, tomorrow 11.12 we have a special event during our class time.
Following my announcement in class last week and on the website, I would like to remind you that we have special
tutorials between 3:30 and 5:30 tomorrow . Below (In parentheses) you will see the locations of each tutorial
Notice that tutorial A and B are an hour and C and D our two hours each.
Overall A and B are more suitable for non biology background but you are welcome to choose.
If you choose C or D they ask to bring laptops with you as there will be hands on practice.
All tutorials are in English
A. 15:30-16:30 Noam Kaplan (Emerson 4-17) Studying the genome in 1D and 3D with Hi-C
B. 16:30-17:30 Uri Shalit (Emerson 4-17) Mining Electronic Medical Records
C. 15:30-17:30 Nathan Salomonis (Physics, Room 333, Ledov Bldg.) Using AltAnalyze for automated discovery of single-cell RNA-Seq profiles from raw sequencing data
D. 15:30-17:30 Artem Barski (Physics Room 377, Ledov Bldg. ) ChIP-Seq/Epigenomics data analysis with BioWardrobe
VERY IMPORTANT our class tutorial by Rachelly will be taking place as usual, same place and times as every week
DON'T MISS THEM.
Yael and class staff
HW3 is published
HW3 is now on the site.
Due date is December 26th.
Next week special events
As I discussed with you in class on Monday, next week we have a special Bioinformatics event in campus.
As part of the course you are expected to join one of the bioinformatics tutorial that will take place on Monday
Dec 11th at 3:30 (instead of the regular class) in the biotechnology building.
Exact place will be announced later this week.
The list of tutorial (you should choose one) can be found here:
At this stage you are requested to register to the bootcamp
Registeration (Free) is here: http://biomedical-informatics.net.technion.ac.il/registration/
More information will be provided later.
IMPORTANT the regular tirgulim with Rachelly will be as usual
Have a good week
The course staff
FAQ for HW2
FAQ for HW2 was published. Please be sure to get updated on all Q&As published in it before you submit your HW solutions.
HW2 was now published in the site. The deadline is December 5th.
Reminding you that questions regarding the HW should be referred to Alona only.
FAQ for HW1 is published
FAQ for HW1 is now published on the site.
It is your responsibility to check the FAQ from now on and follow the instructions in it, as you will be graded by it.
Have a nice week,
Clarification about asking questions regarding HW
The answering time you should expect when sending a question regarding HW is 2-3 days, weekends not included!
You should NOT send repeated e-mails every few hours to Alona, checking why she is not answering, and if it is not clear you - should be POLITE in your mails.
From the next assignment, questions will not be answered in the last 24 hours prior to submission deadline.
Be sure to start the HW on time, and ask your questions early. In addition, you depend on online tools they may take a while to run.
HW 1 published
HW 1 was now published in the course site.
The due date is November 20th. Submission is in pairs and should be done through the course site.
Please submit only one solution per pair, and make sure that the students names and IDs appear at the solution file.
All questions regarding the HW should be sent to Alona, the HW checker ( ). Yael and Rachelly will not be answering questions regarding thee HW.
Signing up for pairs - last notice
Whomever doesn't register until tonight for the pairs - will not be able to attend the course, even if he/ she is currently registered for it.
So if there is still anyone who didn't register in the google doc, please to so today.
Signing up for pairs
We want to remind you again to sign up for the pairs in the google form: https://docs.google.com/forms/d/e/1FAIpQLSeuy5ojBxNinqyC07Mwz4W7Pnj8wEHDwYwQ38blMOcek__MFg/viewform?usp=sf_link
Please do this ASAP as this affects other students that want to register to the course or are looking for a partner.
Signing up for pairs
For the course you will have to submit 4 HW assignments and a final project. The work on the HW and project will be done in pairs.
We highly recommend for you to pair up with a partner from a different faculty - one from computer science and the other from biology-oriented faculty.
To find partners, you can use the "Find a Partner" tab on the course site. Anyone needing additional help finding a partner can also write to me ( ), please state what faculty you are from.
To register for pairs, please fill in the following google form. Please fill it in in English, and only once per pair:
The first HW will be published in 2 weeks, so the pair registration deadline is November 4th.
Have a nice day,
Sherman building location
Please notice that the Sherman building in which we teach is the Education in Science Faculty,
near the Biology Faculty.
Room 107 is one floor down from the entrance - it is the auditorium on your left.
See you soon,
Welcome to "Introduction to Bioinformatics"
Welcome to the "Introduction to Bioinformatics" course.
The first tutorial will be for CS students only and will include relevant background in biology needed for the course.
Good luck in the upcoming semester,