Clarification regarding the submission of the final project related files. | |
| Dear students, You should submit your final project in PDF and the Rmd file with all the relevant code at the same format as you did with your homework. You submit it on site in a ZIP folder with your IDs in a homework format. What about all the data files you worked with ? In the PDF file of your final project, in the Methods section, you'll put a link to a folder with all the relevant data files you worked with, that will allow us to run your code. The link can be to Dropbox, OneDrive, Git, etc. Good luck, Alona |
| עדכון אחרון ב- 24/8/2021, 15:45:24 Last updated on 24/8/2021, 15:45:24 Последняя модификация 24/8/2021, 15:45:24 تمت الحتلنة الأخيرة ب- 24/8/2021, 15:45:24 |
The deadline for the project submission is postponed | |
| Dear students, We postpone the final project submission date to 5.9 at 23:59. Best regards, Alona |
| פורסם ב- 18/8/2021, 11:29:06 Created on 18/8/2021, 11:29:06 Создано 18/8/2021, 11:29:06 تم النشر ب- 18/8/2021, 11:29:06 |
Workflow submission list | |
| Dear students, Each pair was assigned to Dvir or to Alona for the workflow submission. Please find the IDs of your pair (only the last 3 digits of each ID were included) in the workflow submission list under the Final Project section and submit your workflow accordingly. If you don't find yourself on the list please write me ASAP. Best, Alona |
| פורסם ב- 15/7/2021, 12:37:46 Created on 15/7/2021, 12:37:46 Создано 15/7/2021, 12:37:46 تم النشر ب- 15/7/2021, 12:37:46 |
Office hour canceled | |
| Hi, Due to unfortunate circumstances, Dr. Rabner's office hour today is canceled. Alona will contact later those who set a time. Best, Dvir |
| פורסם ב- 24/6/2021, 14:14:09 Created on 24/6/2021, 14:14:09 Создано 24/6/2021, 14:14:09 تم النشر ب- 24/6/2021, 14:14:09 |
Packages installation for Tutorial 12 | |
| Dear students, Please find the packages installation instructions in the Tutorial 12 section. Best, Alona |
| פורסם ב- 21/6/2021, 07:09:54 Created on 21/6/2021, 07:09:54 Создано 21/6/2021, 07:09:54 تم النشر ب- 21/6/2021, 07:09:54 |
Clarifications for HW4 | |
| Dear students, At 1.2 compare by "cancer type", not by "tumor type". Also, answer which cancer type has the lowest median of overall survival time ? At 1.4, 1.6 refer to four cancers analyzed. Best, Alona |
| פורסם ב- 15/6/2021, 13:55:45 Created on 15/6/2021, 13:55:45 Создано 15/6/2021, 13:55:45 تم النشر ب- 15/6/2021, 13:55:45 |
Packages installation for Tutorial 11 | |
| Dear students, Today we will do a tutorial on the Seurat package. For this matter please install 2 packages by: install.packages('patchwork') install.packages('Seurat') Best, Alona |
| פורסם ב- 14/6/2021, 09:24:04 Created on 14/6/2021, 09:24:04 Создано 14/6/2021, 09:24:04 تم النشر ب- 14/6/2021, 09:24:04 |
HW4 is published | |
| Dear students, HW4 is published, the due date is 1.7. Best, Alona |
| פורסם ב- 13/6/2021, 14:08:06 Created on 13/6/2021, 14:08:06 Создано 13/6/2021, 14:08:06 تم النشر ب- 13/6/2021, 14:08:06 |
Back in class | |
| Hi, The lecture halls are open again, so today the lecture and the recitation will be in class. The lecture today will be between 12:30-13:50 without a break. See you soon, Dvir |
| פורסם ב- 7/6/2021, 10:57:34 Created on 7/6/2021, 10:57:34 Создано 7/6/2021, 10:57:34 تم النشر ب- 7/6/2021, 10:57:34 |
Guest lecture | |
| Hi, This week we will have an exciting guest lecturer - Prof. Yaniv Erlich - who will talk about how to store data in DNA and capture criminals. Prof. Erlich led a lab at Columbia University in computational genomics, but decided to come back to Israel a couple of years ago. He currently splits his time between being a founder and the CEO of Eleven Therapeutics, the CSO of MyHeritage, and teaching at IDC. The lecture will take place on zoom **only** and will be between 13:00-14:00. We ask that you make the effort and join the online meeting. Also, please open your camera. I plan to open the zoom session at 12:30, and you are welcome to join and chat about things you would like to ask or share. Best, Dvir |
| פורסם ב- 29/5/2021, 21:29:57 Created on 29/5/2021, 21:29:57 Создано 29/5/2021, 21:29:57 تم النشر ب- 29/5/2021, 21:29:57 |
Clarification for HW3 | |
| Dear students, Please pay attention that you should use MAF=0.1 for the calculation at Question 1, 5.4. Best, Alona |
| פורסם ב- 26/5/2021, 15:38:14 Created on 26/5/2021, 15:38:14 Создано 26/5/2021, 15:38:14 تم النشر ب- 26/5/2021, 15:38:14 |
HW3 is published | |
| Dear students, HW3 is published. Best, Alona |
| פורסם ב- 25/5/2021, 12:35:21 Created on 25/5/2021, 12:35:21 Создано 25/5/2021, 12:35:21 تم النشر ب- 25/5/2021, 12:35:21 |
Packages installation for Tutorial 8 | |
| Dear students, The package installation instructions for the next lesson are in the Tutorial 8 section. Best, Alona |
| פורסם ב- 23/5/2021, 22:31:57 Created on 23/5/2021, 22:31:57 Создано 23/5/2021, 22:31:57 تم النشر ب- 23/5/2021, 22:31:57 |
Lecture and recitations will be online only tomorrow | |
| Dear students, As you probably already know, the Taub building is under construction and all in-class lectures are canceled until next week. The lecture and recitations will be on their regular times **online only** using the regular zoom links. There will be two recitations (14:30 and 15:30). See you tomorrow (online), Dvir |
| פורסם ב- 23/5/2021, 18:45:25 Created on 23/5/2021, 18:45:25 Создано 23/5/2021, 18:45:25 تم النشر ب- 23/5/2021, 18:45:25 |
HW#2 - submission extension | |
| Dear students, Due to the situation, we are extending the submission deadline of HW#2 to Thursday, May 27 at 23:59. Please note that this extension does will not affect the timeline of the other exercises. HW#3 will be published on Monday. Dr. Rabner will prioritize questions regarding HW#3 in her office hours on Wednesday. Best, Dvir |
| פורסם ב- 20/5/2021, 15:45:59 Created on 20/5/2021, 15:45:59 Создано 20/5/2021, 15:45:59 تم النشر ب- 20/5/2021, 15:45:59 |
Feedback - halfway | |
| Hi all, We just passed halfway through the course and we would love to get some feedback from you. Please fill out this form: https://forms.gle/CfMVQUtqsQikB3ar6 The form is anonymous. Thanks, Dvir |
| עדכון אחרון ב- 11/5/2021, 22:08:27 Last updated on 11/5/2021, 22:08:27 Последняя модификация 11/5/2021, 22:08:27 تمت الحتلنة الأخيرة ب- 11/5/2021, 22:08:27 |
Packages installation for Tutorial 7 | |
| Dear students, The package installation instructions for the next lesson are in the Tutorial 7 section. Please pay attention that our FAQs section is alive, I'll put there the answers to some of your questions regarding HW and some additional clarifications if will be needed. Pay attention that you consider the answers that were given there before sending me a question. Best, Alona |
| פורסם ב- 9/5/2021, 10:26:16 Created on 9/5/2021, 10:26:16 Создано 9/5/2021, 10:26:16 تم النشر ب- 9/5/2021, 10:26:16 |
Packages installation for Tutorial 6 | |
| Dear students, The packages required for tutorial 6 can be found in the Tutorial 6 section. You can install them directly from the markdown file attached there by the order specified in the file. See you tomorrow, Alona |
| פורסם ב- 2/5/2021, 15:06:34 Created on 2/5/2021, 15:06:34 Создано 2/5/2021, 15:06:34 تم النشر ب- 2/5/2021, 15:06:34 |
The tutorial recording and the markdown | |
| Dear students, The tutorial recording was published, please pay attention that there were slight changes in the wording of the markdown (not the code). The updated version of the markdown is under the Tutorial 5 section and you are welcome to download it. Sorry for the inconvenience and hope to see you next week. Best, Alona |
| פורסם ב- 28/4/2021, 21:00:51 Created on 28/4/2021, 21:00:51 Создано 28/4/2021, 21:00:51 تم النشر ب- 28/4/2021, 21:00:51 |
The tutorial today is cancelled | |
| Dear students, Unfortunately, I have to cancel our tutorial sessions today, both frontal and zoom. All the material for the tutorial today is in the Tutorial 5 section. The recorded tutorial will be published today in the evening or tomorrow. You can address your questions regarding the material in the tutorial by sending me an email. Best regards, Alona |
| פורסם ב- 26/4/2021, 12:06:41 Created on 26/4/2021, 12:06:41 Создано 26/4/2021, 12:06:41 تم النشر ب- 26/4/2021, 12:06:41 |
Packages installation for Tutorial 5 | |
| Dear students, The packages required for tutorial 5 can be found in the Tutorial 5 section. You can install them directly from the markdown file attached there. Best, Alona |
| פורסם ב- 26/4/2021, 09:19:56 Created on 26/4/2021, 09:19:56 Создано 26/4/2021, 09:19:56 تم النشر ب- 26/4/2021, 09:19:56 |
Finding a partner for HW and project submission | |
| Dear students, If you didn't find your partner for the HW and project submission yet, please use the "חיפוש שותפים" section or write me directly ASAP and I will match between you. Best, Alona |
| פורסם ב- 20/4/2021, 17:54:46 Created on 20/4/2021, 17:54:46 Создано 20/4/2021, 17:54:46 تم النشر ب- 20/4/2021, 17:54:46 |
Packages installation for Tutorial 4 | |
| Dear students, To be able to run the code at our next tutorial you will need to install three additional packages from CRAN. The installation instructions can be found in the Tutorial 4 section. Please make sure that all the previously mentioned packages are already installed. Best, Alona |
| פורסם ב- 18/4/2021, 21:15:59 Created on 18/4/2021, 21:15:59 Создано 18/4/2021, 21:15:59 تم النشر ب- 18/4/2021, 21:15:59 |
Short lecture today | |
| Dear students, As mentioned last lecture, today we will meet for only 45 minutes (12:30-13:15). The recording of the other half is available for you in the course materials. Best, Dvir |
| פורסם ב- 12/4/2021, 10:36:38 Created on 12/4/2021, 10:36:38 Создано 12/4/2021, 10:36:38 تم النشر ب- 12/4/2021, 10:36:38 |
Additional package for tutorial 3 | |
| Dear students, The most important package for Tutorial 3 is the markdown package. In case you didn't install this package yet, the updated instructions are in the instructions file. Best, Alona |
| פורסם ב- 11/4/2021, 22:13:48 Created on 11/4/2021, 22:13:48 Создано 11/4/2021, 22:13:48 تم النشر ب- 11/4/2021, 22:13:48 |
Packages installation for Tutorial 3 | |
| Dear students, To be able to run the code at our next tutorial you will need to install a Bioconductor and a few additional packages. Detailed instructions regarding the installation of all of the aforementioned can be found in the course material in the Tutorial 3 section. Please make sure you first install Bioconductor and then the following packages: IRanges GenomicRanges MSA BSgenome.Hsapiens.UCSC.hg19 seqinr ape Please pay attention that installation of few packages may take a while, so please arrange accordingly. Best, Alona |
| פורסם ב- 11/4/2021, 21:06:42 Created on 11/4/2021, 21:06:42 Создано 11/4/2021, 21:06:42 تم النشر ب- 11/4/2021, 21:06:42 |
מצלמה בשיעורים | |
| בכיתה טאוב 2 לא ניתן לכוון את המצלמה בזום על המרצה. בשיעור הראשון הפעלתי את המצלמה מהמחשב האישי ולא השתמשתי במצלמה שבכיתה. בשיעור השני השתמשתי במצלמה של הכיתה. זוהי שאלה לסטודנטים המתחברים מהזום (או צופים בהקלטות של השיעורים) - אודה אם תוכלו לענות על הסקר - https://forms.gle/DfuhtEAn9BNYLfir9 |
| עדכון אחרון ב- 7/4/2021, 13:35:06 Last updated on 7/4/2021, 13:35:06 Последняя модификация 7/4/2021, 13:35:06 تمت الحتلنة الأخيرة ب- 7/4/2021, 13:35:06 |
Course registration | Zoom links | |
| Dear students, 1. We opened more slots for students to sign for the course. If you have not already registered, please do it as soon as possible, as space is limited. 2. Zoom links for the lecture and tutorial are available under "Course materials" (חומר הקורס). See you later today. Best, Dvir |
| פורסם ב- 22/3/2021, 10:43:50 Created on 22/3/2021, 10:43:50 Создано 22/3/2021, 10:43:50 تم النشر ب- 22/3/2021, 10:43:50 |
Your intention to come to lecture/tutorial in-person or to participate in Zoom | |
| Dear students, To allow us an optimal teaching experience and to allow you an optimal learning experience please fill up a very short doodle regarding your intention to come to lecture/tutorial in-person or to participate in Zoom. https://doodle.com/poll/dy8fnskpqdatgdxx?utm_source=poll&utm_medium=link Thank you, Alona |
| עדכון אחרון ב- 19/3/2021, 15:10:35 Last updated on 19/3/2021, 15:10:35 Последняя модификация 19/3/2021, 15:10:35 تمت الحتلنة الأخيرة ب- 19/3/2021, 15:10:35 |
Hybrid and in-person teaching | |
| Dear Students, The lecture on Monday will be given at hybrid teaching format, meaning that the lecture will be given in-person and simultaneously online at Zoom and will be recorded. Please pay attention that the class is very spacious and there is enough room for all the students at the course. After the lecture, you have a tutorial. The tutorial at 14:30-15:30 is given in-person only. The tutorial at 15:30-16:30 is given in hybrid teaching format: in-person, and online at Zoom and will be recorded. If you want to gain the maximal attention at in-person tutorial, you are cordially invited to attend the tutorial at 14:30-15:30, as at hybrid tutorial my attention will be split between online and in-person teaching. The links to the Zoom lecture and tutorial will be published a short while before the lecture and the tutorial. Have a nice weekend, Alona |
| עדכון אחרון ב- 18/3/2021, 18:28:38 Last updated on 18/3/2021, 18:28:38 Последняя модификация 18/3/2021, 18:28:38 تمت الحتلنة الأخيرة ب- 18/3/2021, 18:28:38 |
A required software for the tutorials and a kind reminder | |
| Dear students, In our course you will be working with biological data and for this purpose, we will use R - programming language, and RStudio, a user-friendly application that allows you to get the best R can give you in data analysis. You are cordially requested to make sure that both R and RStudio are installed on your computer, as we will start learning R at our first tutorial. Please follow the instructions in this link https://rstudio-education.github.io/hopr/starting.html in order to install both R and RStudio. The next stage is packages installation. R packages are similar to libraries in C/C++. Please take a few minutes to understand the concept of packages as described at: https://rstudio-education.github.io/hopr/packages2.html . For our first lessons, you’ll need to install tidyverse collection of packages that includes most of the packages that you’re likely to use in data analyses (such as ggplot2, dplyr, stringr etc.). Install all the packages in the tidyverse by running install.packages("tidyverse") command in the Console window. You can read about different packages in the tidyverse here: https://www.tidyverse.org/packages/ . Please make sure that RStudio is installed at your computer altogether with R and the required packages before the first tutorial to allow you a convenient hands-on experience. Another issue - thanks to everybody who filled up the questionnaire, everyone that didn't manage to do it - please find a few minutes to tell us about yourself and your expectations. Best, Alona |
| פורסם ב- 17/3/2021, 11:14:49 Created on 17/3/2021, 11:14:49 Создано 17/3/2021, 11:14:49 تم النشر ب- 17/3/2021, 11:14:49 |
Questionnaire | |
| We hope you enjoyed watching the documentary (and if not, highly recommended). Before we start the semester we want to know you better. It would help us understand what is your background and what you hope to gain from this course. Please fill out the following questionnaire: https://forms.gle/xGxbP5EgPWt2Gks88 Best, Dvir and Alona |
| פורסם ב- 15/3/2021, 13:29:17 Created on 15/3/2021, 13:29:17 Создано 15/3/2021, 13:29:17 تم النشر ب- 15/3/2021, 13:29:17 |
הגן: היסטוריה אינטימית | The Gene: An Intimate History | |
| I'm very excited to start the semester in a couple of weeks. Before the semester begins, I would like to recommend a documentary by Ken Burns, which is based on the book "The Gene" by Siddhartha Mukherjee: https://www.youtube.com/watch?v=ea5T6WFc9po We will discuss many of the subjects mentioned in this documentary, and it is recommended to watch it before the course begins. Note that the movie is 4 hours long. Enjoy, Dvir |
| עדכון אחרון ב- 4/3/2021, 13:45:08 Last updated on 4/3/2021, 13:45:08 Последняя модификация 4/3/2021, 13:45:08 تمت الحتلنة الأخيرة ب- 4/3/2021, 13:45:08 |
Waiting list for the course "Introduction to Bioinformatics" (236523) | |
| We now have over 70 students already signed up for the course. This is great, and I hope you are excited as I am to start the semester. Since the capacity of the course is limited, we had to stop the enrolment. However, there are many students that are interested in enrolling, and we are trying to find a solution. No promises for now. If you want to sign up for the waiting list, please fill out this form - https://cutt.ly/zjnGHbd . Please do not fill it you are already enrolled. Best, Dvir |
| עדכון אחרון ב- 13/1/2021, 11:32:10 Last updated on 13/1/2021, 11:32:10 Последняя модификация 13/1/2021, 11:32:10 تمت الحتلنة الأخيرة ب- 13/1/2021, 11:32:10 |