BioMicroCenter:BioinfoClasses: Difference between revisions

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==Teaching Schedule==
== REGISTRATION INFORMATION ==
 
Registration for bioinformatcs sessions is managed using the <b>[https://mit.ilabsolutions.com/ Koch Institute iLabs instance]</b>. Courses are restricted to members of the MIT community and [https://ist.mit.edu/prisma/globalprotect MIT VPN] is required to access course materials. <BR>
* If you already have an account you can directly access the registration form [https://mit-ki.ilabsolutions.com/service_item/new/3189?spt_id=21294 with this link].<BR>
* If you do not have an ilabs account, [https://ki.mit.edu/sbc/bioinformatics/access instructions are here]. Please follow the steps in the document. As part of registration, you will need to select your PI from a dropdown menu and your PI or their designated group manager will need to approve the membership request and assign to you an MIT cost object before you can submit a request for training. Note: the BioMicro Center cannot do this for you. IF your PI is not listed in the dropdown menu, you will need to contact us with the PI name, MIT kerberos, cost object to be charged for the course fee, and the PI’s designated group manager name and MIT Kerberos. Individuals without a PI/cost object are not eligable for registration.
 
 
 
 
==Classes in fall 2023==
 
{| border=1
!width 150px align="center"|DATE
!width 150px align="center"|TIME
!width 150px align="center"|Instructor
!width 150px align="center"|Location
!width 150px align="center"|Room
!width 150px align="center"|Topic
|-align="center"
|Monday September 18th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 56
|56-602
|Introduction to Linux and Cluster Computing
|-align="center"
|Tuesday September 26, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 56
|56-602
|Introduction of Python to biologists session I
|-align="center"
|Wednesday September 27, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-659
|Introduction of Python to biologists session II
|-align="center"
|Thursday September 28, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-559
|Introduction to Biopython
|-align="center"
|Monday October 16, 2023
|2:00pm-4:30pm
|Allen Soberanes & Duanduan Ma
|Building 76
|76-259
|Introduction to Linux and Cluster Computing
|-align="center"
|Monday October 23th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-259
|Data processing and visualization using Python: Introduction to Pandas
|-align="center"
|Tuesday October 24th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-659
|Data processing and visualization using Python: Introduction to Matplotlib
|-align="center"
|Wednesday October 25th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-359
|Data processing and visualization using Python: Introduction to Seaborn
|-align="center"
|Monday November 13th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-259
|Introduction of machine learning and its applications in biology. session I
|-align="center"
|Tuesday November 14th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-659
|Introduction of machine learning and its applications in biology. session II
|-align="center"
|Monday November 27th, 2023
|2:00pm-4:30pm
|Allen Soberanes & Duanduan Ma
|Building 76
|76-259
|Introduction to Unix and cluster computing
|-align="center"
|Monday December 12th, 2023
|2:00pm-4:30pm
|Charlie Demurjian
|TBD
|TBD
|Data Deposition in Public Repositories
|}
 
 
 
==Previous teaching==
 
{| border=1  
{| border=1  
  !width 150px align="center"|DATE
  !width 150px align="center"|DATE
Line 184: Line 291:
  |Introduction to UNIX and the KI/BioMicro computational resources
  |Introduction to UNIX and the KI/BioMicro computational resources
  |-align="center"
  |-align="center"
  |Fri Feb 3, 2016
  |Fri Feb 3, 2017
  |12:00pm-2:00pm
  |12:00pm-2:00pm
  |Charlie Whittaker and Duanduan Ma
  |Charlie Whittaker and Duanduan Ma
Line 209: Line 316:
  |Duanduan Ma
  |Duanduan Ma
  |Building 68
  |Building 68
  |68-
  |68-374
  |Introduction to Python  
  |Introduction to Python
|}
|-align="center"
 
|Mon June 5, 2017
   
|1pm-4pm
 
|Duanduan Ma
                            Introduction to Python
|Building 68
                            Monday, April 24, 2017
|68-121
                              1:00-4:00 PM
|Introduction to Python
                                  68-574
|-align="center"
   
|Mon July 10, 2017
This hands-on session will introduce Python as a scripting tool for analyzing data. The topics will include basics to program in Python as well as using existing tools in Biopython. Course size will be limited but future classes covering similar topics will be scheduled basing on demands.
|1pm-4pm
   
|Duanduan Ma
Please contact Duan Ma (duan@mit.edu) to sign up. Registration will close at 5pm on Friday, April 21, 2017.
|Building 76
|76-559
|Introduction to Python
|-align="center"
|Mon Aug 28, 2017
|2pm-4pm
|Duanduan Ma
|Building 68
|68-374
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon Sep 25, 2017
|2:00pm-3:00pm
|Vincent Butty
|Building 68
|68-181
|RNA-Seq Experimental design + QC ; Slides [https://www.dropbox.com/s/p0mj0jubnuf6tm1/2017-RNASeqTrainingSession1.pdf?dl=0]
|-align="center"
|Mon Oct 2, 2017
|1:00pm-2:00pm
|Vincent Butty
|Building 68
|68-181
|RNA-Seq analysis ; Slides [https://www.dropbox.com/s/wojp2n5gy72vzn1/RNASeq_Tranining_pt2_100217.pdf?dl=0]
|-align="center"
|Mon Nov 13, 2017
|2pm-4pm
|Duanduan Ma
|Building 76
|76-259
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon Dec 11, 2017
|1pm-4pm
|Duanduan Ma
|Building 56
|56-602
|Introduction to R
|-align="center"
|Wed Jan 31, 2018
|10am-12pm
|Charlie Whittaker
|Building 14N (DIRC)
|14N-132
|Gene Set Enrichment Analysis
|-align="center"
|Mon Feb 12, 2018
|1pm-4pm
|Duanduan Ma
|Building 76
|76-459
|Introduction to R
|-align="center"
|Mon Mar 12, 2018
|2pm-4pm
|Duanduan Ma
|Building 56
|56-602
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon Apr 23, 2018
|1:30pm-2:30pm
|Duanduan Ma
|Building 68
|68-181
|Introduction to Biopython
|-align="center"
|Mon May 14, 2018
|2:30pm-3:30pm
|Duanduan Ma
|Building 76
|76-259
|Introduction to Biopython
|-align="center"
|Mon June 11, 2018
|2:00pm-4:00pm
|Duanduan Ma
|Building 56
|56-602
|Introduction to UNIX and the KI/BioMicro computational resourceso Biopython
|-align="center"
|Mon July 16, 2018
|2:30pm-4:00pm
|Duanduan Ma
|Building 68
|68-121
|Introduction of Python to biologists session 1
|-align="center"
|Mon August 13, 2018
|2:30pm-4:00pm
|Duanduan Ma
|Building 76
|76-559
|Introduction of Python to biologists session 2
|-align="center"
|Mon September 10, 2018
|2:00pm-4:00pm
|Duanduan Ma
|Building 56
|56-602
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Tue October 23, 2018
|1:30pm-2:30pm
|Vincent Butty
|Building 68
|68-181
|A Traveler's companion to RNA-Seq interpretation session 1 - Slides [https://www.dropbox.com/s/0l8qzsl2eur8357/2018-RNASeqTrainingSession1.pdf?dl=0]
|-align="center"
|Mon November 5, 2018
|1pm-2pm
|Vincent Butty
|Building 68
|68-181
|A Traveler's companion to RNA-Seq interpretation session 2 - Slides [https://www.dropbox.com/s/o229bslzkoprf0a/RNASeq_Tranining_pt2_110518.pdf?dl=0]
|-align="center"
|Mon December 10, 2018
|2:00pm-4:00pm
|Duanduan Ma
  |Building 76
|76-259
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Thursday Jan 31, 2019
|10am-12pm
|Charlie Whittaker
|Building 14N (DIRC)
|14N-132
|Gene Set Enrichment Analysis
|-align="center"
|Mon February 11, 2019
|2:30pm-4:00pm
|Duanduan Ma
|Building 68
|68-674
|Introduction of Python to biologists session 1
|-align="center"
|Mon March 11, 2019
|2:30pm-4:30pm
|Duanduan Ma
|Building 76
|76-259
|Introduction of Python to biologists session 2
|-align="center"
|Mon April 8, 2019
|2:00pm-4:00pm
|Duanduan Ma
|Building 68
|68-180
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon May 13, 2019
|2pm-4pm
|Duanduan Ma
|Building 68
|68-121
|Introduction to R session 1
|-align="center"
|Mon June 10, 2019
|2pm-4pm
|Duanduan Ma
|Building 76
|76-659
|Introduction to R session 2
|-align="center"
|Mon July 8, 2019
|2:00pm-4:00pm
|Duanduan Ma
|Building 68
|68-574
  |Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Tue August 27, 2019
|2:30pm-3:30pm
|Jingzhi Zhu & Duanduan Ma
|Building 76
|76-659
|How to install software packages yourself on computing clusters
|-align="center"
|Wed September 25, 2019
|1:00pm-2:00pm
|Vincent Butty
|Building 68
|68-181
|A Traveler's companion to RNA-Seq interpretation session 1 - Slides [https://www.dropbox.com/s/0swr3trx0tq6ylf/2019-RNASeqTrainingSession1_092519.pdf?dl=0]
|-align="center"
|Wed October 2, 2019
|1:00pm-2:00pm
|Vincent Butty
|Building 68
|68-181
|A Traveler's companion to RNA-Seq interpretation session 2 - Slides [https://www.dropbox.com/s/43a3wgeur3gvmjg/RNASeq_Tranining_pt2_100219_prePPT.pdf?dl=0]
|-align="center"
|Mon November 18, 2019
|2:00pm-4:00pm
|Duanduan Ma
|Building 76
|76-659
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Tues December 10, 2019
|1:00pm-2:00pm
|BMC/IGB core (Vincent Butty)
|Building 68
|68-181
|Single Cell RNA-Seq Slides: [https://www.dropbox.com/s/ow5g18egngupipu/scRNASeq_December10.pdf?dl=0]
  |-align="center"
|Mon January 31, 2020
|2:00pm-3:30pm
|Duanduan Ma
|Building 76
|76-659
|Introduction of machine learning and its applications in biology
|-align="center"
|Mon February 10, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Building 76
|76-659
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon March 9, 2020
|2:30pm-4:00pm
|Duanduan Ma
|Building 76
|76-659
|Introduction of Python to biologists session 1
|-align="center"
|Mon April 17, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Fri May 8, 2020
|1:00pm-3:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 1
|-align="center"
|Wed May 13, 2020
|1:00pm-3:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 2
|-align="center"
|Fri May 27, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session 2
|-align="center"
|Fri June 5, 2020
|2:00pm-4:00pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session 1
|-align="center"
|Mon June 8, 2020
|2:00pm-4:00pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session 2
|-align="center"
|Mon June 15, 2020
|2:00pm-4:00pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Biopython
|-align="center"
|Mon July 20, 2020
|2:00pm-4:00pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon September 14, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of machine learning and its applications in biology session I
|-align="center"
|Mon September 21, 2020
|2:00pm-4:30pm
|Duanduan Ma and Huiming Ding
|Zoom
|Zoom link
|Introduction of machine learning and its applications in biology session II
|-align="center"
|Mon October 19, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Mon October 26, 2020
|2:00pm-4:30pm
|Jingzhi Zhu
|Zoom
|Zoom link
|How to install software packages yourself on computing clusters
|-align="center"
|Mon November 9, 2020
|2:00pm-4:30pm
|Dikshant Pradhan
|Zoom
|Zoom link
|Public Data Repositories
|-align="center"
|Wed December 9, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 1
|-align="center"
|Wed December 16, 2020
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 2
|-align="center"
|Tuesday February 16, 2021
|2pm-4:30pm
|Duanduan Ma
|zoom
|zoom link
|Introduction to UNIX and the KI/BioMicro computational resources session I
|-align="center"
|Monday February 22, 2021
|2pm-4:30pm
|Jingzhi Zhu, Duanduan Ma
|zoom
|zoom link
|Introduction to UNIX and the KI/BioMicro computational resources session II
|-align="center"
|Monday March 15, 2021
|2pm-4:30pm
|Duanduan Ma
|zoom
|zoom link
|Introduction of Python to biologists session I
|-align="center"
|Monday March 22, 2021
|2pm-4:30pm
|Duanduan Ma
|zoom
|zoom link
|Introduction of Python to biologists session II
|-align="center"
|Monday March 29, 2021
|2pm-4:30pm
|Duanduan Ma
|zoom
|zoom link
|Introduction to Biopython
|-align="center"
|Monday April 12, 2021
|2pm-3pm
|Vincent Butty
|zoom
|zoom link
|A Traveler's companion to RNA-Seq interpretation session I
|-align="center"
|Monday April 26, 2021
|2pm-3pm
|Vincent Butty
|zoom
|zoom link
|A Traveler's companion to RNA-Seq interpretation session II
|-align="center"
|Monday May 3, 2021
|2pm-3pm
|Vincent Butty
|zoom
|zoom link
|Single Cell RNA-seq
|-align="center"
|Monday May 10, 2021
|2pm-4:30pm
|Duanduan Ma
|zoom
|zoom link
|Introduction to UNIX and the KI/BioMicro computational resources session I
|-align="center"
|Monday May 17, 2021
|2pm-4:30pm
|Jingzhi Zhu, Duanduan Ma
|zoom
|zoom link
|Introduction to UNIX and the KI/BioMicro computational resources session II
|-align="center"
|Monday June 7, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 1
|-align="center"
|Monday June 14, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 2
|-align="center"
|Monday September 13, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to UNIX and the KI/BioMicro computational resources
|-align="center"
|Monday September 20, 2021
|2:00pm-4:30pm
|Jingzhi Zhu
|Zoom
|Zoom link
|Effective utilization of IGB computational resources - SLURM & CONDA
|-align="center"
|Monday October 11, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Python session I
|-align="center"
|Monday October 18, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Python session II
|-align="center"
|Monday October 25, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Biopython
|-align="center"
|Monday November 1, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Pandas
|-align="center"
|Monday November 8, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Matplotlib
|-align="center"
|Monday November 15, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Seaborn
|-align="center"
|Monday December 13, 2021
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Linux and the IGB computational resources
|-align="center"
|Tuesday February 8, 2022
|2:00pm-4:30pm
|Duanduan Ma and Jingzhi Zhu
|Zoom
|Zoom link
|Introduction to Linux and the KI/BioMicro computational resources
|-align="center"
|Thursday March 3rd, 2022
|2:00pm-3:00pm
|Dikshant Pradhan
|Zoom
|Zoom link
|Public Data Repositories
|-align="center"
|Monday March 14th, 2022
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|RNA-Seq Design and Analysis Session I
|-align="center"
|Tuesday March 15th, 2022
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|RNA-Seq Design and Analysis Session II
|-align="center"
|Thursday March 17th, 2022
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|RNA-Seq Design and Analysis Session III
|-align="center"
|Monday March 28, 2022
|1:00pm-3:30pm
|Duanduan Ma and Jingzhi Zhu
|Zoom
|Zoom link
|Introduction to Linux and the KI/BioMicro computational resources
|-align="center"
|Monday April 11, 2022
|1:00pm-3:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 1
|-align="center"
|Wednesday April 13, 2022
|1:00pm-3:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 2
|-align="center"
|Monday Apil 25th, 2022
|1:00pm-3:30pm
|Charlie Whittaker Dikshant Pradhan
|Zoom
|Zoom link
|RNAseq HandsOn session 1
|-align="center"
|Wednesday Apil 27th, 2022
|1:00pm-3:30pm
|Charlie Whittaker Dikshant Pradhan
|Zoom
|Zoom link
|RNAseq HandsOn session 2
|-align="center"
|Friday Apil 27th, 2022
|1:00pm-3:30pm
|Charlie Whittaker Dikshant Pradhan
|Zoom
|Zoom link
|RNAseq HandsOn session 3
|-align="center"
|Monday September 19th, 2022
|2:00pm-4:30pm
|Duanduan Ma Jingzhi Zhu
|Zoom
|Zoom link
|Introduction to Linux and Cluster Computing
|-align="center"
|Monday October 3rd, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session I
|-align="center"
|Tuesday October 4th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session II
|-align="center"
|Friday October 7th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Biopython
|-align="center"
|Monday October 31st, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Matplotlib
|-align="center"
|Wednesday November 2nd, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Pandas
|-align="center"
|Friday November 4th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Data processing and visualization using Python: Introduction to Seaborn
|-align="center"
|Monday November 14th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of machine learning and its applications in biology. session I
|-align="center"
|Wednesday November 16th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of machine learning and its applications in biology. session II
|-align="center"
|Monday December 5th, 2022
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Linux and Cluster Computing
|-align="center"
|Monday February 6th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Linux and Cluster Computing
|-align="center"
|Tuesday February 21, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 1
|-align="center"
|Wednesday February 22, 2023
  |2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to R session 2
|-align="center"
|Mon March 13, 2023
|2:00pm-3:30pm
|Stuart Levine
|Zoom
|Zoom link
|Advanced Excel/Google Sheets for Biologists & Administrators
|-align="center"
|Monday April 3rd, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session I
|-align="center"
|Wednesday April 5th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction of Python to biologists session II
|-align="center"
|Monday April 10th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Version control with Git session I
|-align="center"
|Wednesday April 12th, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Version control with Git session II
|-align="center"
|Monday April 24th, 2023
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|Bulk RNA-Seq Design and Analysis Session I
|-align="center"
|Wednesday April 26th, 2023
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|Bulk RNA-Seq Design and Analysis Session II
|-align="center"
|Thursday April 27th, 2023
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|Single cell RNA-Seq Design and Analysis Session I
|-align="center"
|Friday April 28th, 2023
|1:00pm-3:30pm
|Vincent Butty
|Zoom
|Zoom link
|Single cell RNA-Seq Design and Analysis Session II
|-align="center"
|Monday May 1st, 2023
|2:00pm-4:30pm
|Duanduan Ma
|Zoom
|Zoom link
|Introduction to Linux and Cluster Computing
|-align="center"
|Monday May 15th, 2023
|1:00pm-3:00pm
|Charlie Whittaker
|Zoom
|Zoom link
|RNAseq HandsOn session 1
|-align="center"
|Wednesday May 17th, 2023
|1:00pm-3:00pm
|Charlie Whittaker
|Zoom
|Zoom link
|RNAseq HandsOn session 2
|-align="center"
|Thursday May 18th, 2023
|1:00pm-3:00pm
|Charlie Whittaker
|Zoom
|Zoom link
|RNAseq HandsOn session 3
|}

Latest revision as of 14:11, 19 September 2023

REGISTRATION INFORMATION

Registration for bioinformatcs sessions is managed using the Koch Institute iLabs instance. Courses are restricted to members of the MIT community and MIT VPN is required to access course materials.

  • If you already have an account you can directly access the registration form with this link.
  • If you do not have an ilabs account, instructions are here. Please follow the steps in the document. As part of registration, you will need to select your PI from a dropdown menu and your PI or their designated group manager will need to approve the membership request and assign to you an MIT cost object before you can submit a request for training. Note: the BioMicro Center cannot do this for you. IF your PI is not listed in the dropdown menu, you will need to contact us with the PI name, MIT kerberos, cost object to be charged for the course fee, and the PI’s designated group manager name and MIT Kerberos. Individuals without a PI/cost object are not eligable for registration.



Classes in fall 2023

DATE TIME Instructor Location Room Topic
Monday September 18th, 2023 2:00pm-4:30pm Duanduan Ma Building 56 56-602 Introduction to Linux and Cluster Computing
Tuesday September 26, 2023 2:00pm-4:30pm Duanduan Ma Building 56 56-602 Introduction of Python to biologists session I
Wednesday September 27, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-659 Introduction of Python to biologists session II
Thursday September 28, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-559 Introduction to Biopython
Monday October 16, 2023 2:00pm-4:30pm Allen Soberanes & Duanduan Ma Building 76 76-259 Introduction to Linux and Cluster Computing
Monday October 23th, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-259 Data processing and visualization using Python: Introduction to Pandas
Tuesday October 24th, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-659 Data processing and visualization using Python: Introduction to Matplotlib
Wednesday October 25th, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-359 Data processing and visualization using Python: Introduction to Seaborn
Monday November 13th, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-259 Introduction of machine learning and its applications in biology. session I
Tuesday November 14th, 2023 2:00pm-4:30pm Duanduan Ma Building 76 76-659 Introduction of machine learning and its applications in biology. session II
Monday November 27th, 2023 2:00pm-4:30pm Allen Soberanes & Duanduan Ma Building 76 76-259 Introduction to Unix and cluster computing
Monday December 12th, 2023 2:00pm-4:30pm Charlie Demurjian TBD TBD Data Deposition in Public Repositories


Previous teaching

DATE TIME Instructor Location Room Topic
Mon May 11, 2015 2pm-3pm Duanduan Ma Building 76 76-156a&b Introduction to UNIX and the KI/BioMicro computational resources
Mon Jun 15, 2015 1:30pm-3pm Duanduan Ma Building 68 68-374 Follow Up Course of Introduction to UNIX and the KI/BioMicro computational resources
Mon Jul 13, 2015 10am-11am Charlie Whittaker Building 76 76-156a&b Introduction to Spotfire
Mon Aug 10, 2015 1:30pm-3pm Duanduan Ma Building 56 56-602 Introduction to UNIX and the KI/BioMicro computational resources
Mon Sep 14, 2015 1pm-4pm Duanduan Ma Building 68 68-374 Introduction to Python
Mon Oct 19, 2015 1pm-4pm Duanduan Ma Building 68 68-674 Introduction to Python
Mon Nov 9, 2015 1:30pm-3:30pm Jie Wu and Vincent Butty Building 68 68-181 A Traveller's companion to RNA-Seq interpretation 
 QC slides[1] methods slides [2]
Mon Dec 14, 2015 2pm-4pm Duanduan Ma Building 68 68-474 Introduction to UNIX and the KI/BioMicro computational resources
Thur Jan 7, 2016 1:30pm-4:30pm Duanduan Ma Building 32 32-124 Quantitative Biology Workshop Outreach-Introduction to Python
Fri Jan 29, 2016 9:00am-11:00am Charlie Whittaker and Duanduan Ma Building 14N (DIRC) 14N-132 Visualizing and Accessing Genomic Data Using Publically Available Genome Browsers and Databases
Tue Feb 16, 2016 2:00am-3:00am Sara Strandberg-Qlucore Building 76 76-156B Introduction to Qlucore software
Mon Mar 7, 2016 2pm-4pm Duanduan Ma Building 56 56-602 Introduction to UNIX and the KI/BioMicro computational resources
Mon April 11, 2016 1pm-4pm Duanduan Ma Building 68 68-121 Introduction to R
Mon May 2, 2016 1pm-4pm Duanduan Ma Building 68 68-374 Introduction to R
Mon May 9, 2016 1pm-3pm Qlucore Building 14N(DIRC) 14N-132 Hands on training of Qlucore software
Mon June 6, 2016 2pm-4pm Duanduan Ma Building 68 68-374 Introduction to UNIX and the KI/BioMicro computational resources
Mon Jun 13, 2016 1pm-4pm Duanduan Ma Building 76 76-156A/B Introduction to R
Mon July 11, 2016 1pm-4pm Duanduan Ma Building 56 56-602 Introduction to R
Mon Aug 8, 2016 1pm-4pm Duanduan Ma Building 68 68-374 Introduction to R
Mon Sep 12, 2016 2pm-4pm Duanduan Ma Building 76 76-459 Introduction to UNIX and the KI/BioMicro computational resources
Tue Oct 18, 2016 1pm-3pm Duanduan Ma Building 68 68-274 Introduction to UNIX and the KI/BioMicro computational resources
Mon Nov 7, 2016 1:00pm-2:00pm Jie Wu & Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 1 [3]
Mon Nov 14, 2016 1:00pm-2:00pm Jie Wu & Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 2 [4]
Mon Dec 12, 2016 2pm-4pm Duanduan Ma Building 76 76-259 Introduction to UNIX and the KI/BioMicro computational resources
Thurs Jan 19, 2017 1pm-3pm Duanduan Ma Building 68 68-274 Introduction to UNIX and the KI/BioMicro computational resources
Fri Feb 3, 2017 12:00pm-2:00pm Charlie Whittaker and Duanduan Ma Building 14N (DIRC) 14N-132 Visualizing and Accessing Genomic Data Using Publically Available Genome Browsers and Databases
Mon Mar 13, 2017 2pm-4pm Duanduan Ma Building 68 68-374 Introduction to UNIX and the KI/BioMicro computational resources
Mon April 24, 2017 1pm-4pm Duanduan Ma Building 68 68-574 Introduction to Python
Mon May 1, 2017 1pm-4pm Duanduan Ma Building 68 68-374 Introduction to Python
Mon June 5, 2017 1pm-4pm Duanduan Ma Building 68 68-121 Introduction to Python
Mon July 10, 2017 1pm-4pm Duanduan Ma Building 76 76-559 Introduction to Python
Mon Aug 28, 2017 2pm-4pm Duanduan Ma Building 68 68-374 Introduction to UNIX and the KI/BioMicro computational resources
Mon Sep 25, 2017 2:00pm-3:00pm Vincent Butty Building 68 68-181 RNA-Seq Experimental design + QC ; Slides [5]
Mon Oct 2, 2017 1:00pm-2:00pm Vincent Butty Building 68 68-181 RNA-Seq analysis ; Slides [6]
Mon Nov 13, 2017 2pm-4pm Duanduan Ma Building 76 76-259 Introduction to UNIX and the KI/BioMicro computational resources
Mon Dec 11, 2017 1pm-4pm Duanduan Ma Building 56 56-602 Introduction to R
Wed Jan 31, 2018 10am-12pm Charlie Whittaker Building 14N (DIRC) 14N-132 Gene Set Enrichment Analysis
Mon Feb 12, 2018 1pm-4pm Duanduan Ma Building 76 76-459 Introduction to R
Mon Mar 12, 2018 2pm-4pm Duanduan Ma Building 56 56-602 Introduction to UNIX and the KI/BioMicro computational resources
Mon Apr 23, 2018 1:30pm-2:30pm Duanduan Ma Building 68 68-181 Introduction to Biopython
Mon May 14, 2018 2:30pm-3:30pm Duanduan Ma Building 76 76-259 Introduction to Biopython
Mon June 11, 2018 2:00pm-4:00pm Duanduan Ma Building 56 56-602 Introduction to UNIX and the KI/BioMicro computational resourceso Biopython
Mon July 16, 2018 2:30pm-4:00pm Duanduan Ma Building 68 68-121 Introduction of Python to biologists session 1
Mon August 13, 2018 2:30pm-4:00pm Duanduan Ma Building 76 76-559 Introduction of Python to biologists session 2
Mon September 10, 2018 2:00pm-4:00pm Duanduan Ma Building 56 56-602 Introduction to UNIX and the KI/BioMicro computational resources
Tue October 23, 2018 1:30pm-2:30pm Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 1 - Slides [7]
Mon November 5, 2018 1pm-2pm Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 2 - Slides [8]
Mon December 10, 2018 2:00pm-4:00pm Duanduan Ma Building 76 76-259 Introduction to UNIX and the KI/BioMicro computational resources
Thursday Jan 31, 2019 10am-12pm Charlie Whittaker Building 14N (DIRC) 14N-132 Gene Set Enrichment Analysis
Mon February 11, 2019 2:30pm-4:00pm Duanduan Ma Building 68 68-674 Introduction of Python to biologists session 1
Mon March 11, 2019 2:30pm-4:30pm Duanduan Ma Building 76 76-259 Introduction of Python to biologists session 2
Mon April 8, 2019 2:00pm-4:00pm Duanduan Ma Building 68 68-180 Introduction to UNIX and the KI/BioMicro computational resources
Mon May 13, 2019 2pm-4pm Duanduan Ma Building 68 68-121 Introduction to R session 1
Mon June 10, 2019 2pm-4pm Duanduan Ma Building 76 76-659 Introduction to R session 2
Mon July 8, 2019 2:00pm-4:00pm Duanduan Ma Building 68 68-574 Introduction to UNIX and the KI/BioMicro computational resources
Tue August 27, 2019 2:30pm-3:30pm Jingzhi Zhu & Duanduan Ma Building 76 76-659 How to install software packages yourself on computing clusters
Wed September 25, 2019 1:00pm-2:00pm Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 1 - Slides [9]
Wed October 2, 2019 1:00pm-2:00pm Vincent Butty Building 68 68-181 A Traveler's companion to RNA-Seq interpretation session 2 - Slides [10]
Mon November 18, 2019 2:00pm-4:00pm Duanduan Ma Building 76 76-659 Introduction to UNIX and the KI/BioMicro computational resources
Tues December 10, 2019 1:00pm-2:00pm BMC/IGB core (Vincent Butty) Building 68 68-181 Single Cell RNA-Seq Slides: [11]
Mon January 31, 2020 2:00pm-3:30pm Duanduan Ma Building 76 76-659 Introduction of machine learning and its applications in biology
Mon February 10, 2020 2:00pm-4:30pm Duanduan Ma Building 76 76-659 Introduction to UNIX and the KI/BioMicro computational resources
Mon March 9, 2020 2:30pm-4:00pm Duanduan Ma Building 76 76-659 Introduction of Python to biologists session 1
Mon April 17, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to UNIX and the KI/BioMicro computational resources
Fri May 8, 2020 1:00pm-3:30pm Duanduan Ma Zoom Zoom link Introduction to R session 1
Wed May 13, 2020 1:00pm-3:30pm Duanduan Ma Zoom Zoom link Introduction to R session 2
Fri May 27, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session 2
Fri June 5, 2020 2:00pm-4:00pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session 1
Mon June 8, 2020 2:00pm-4:00pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session 2
Mon June 15, 2020 2:00pm-4:00pm Duanduan Ma Zoom Zoom link Introduction to Biopython
Mon July 20, 2020 2:00pm-4:00pm Duanduan Ma Zoom Zoom link Introduction to UNIX and the KI/BioMicro computational resources
Mon September 14, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of machine learning and its applications in biology session I
Mon September 21, 2020 2:00pm-4:30pm Duanduan Ma and Huiming Ding Zoom Zoom link Introduction of machine learning and its applications in biology session II
Mon October 19, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to UNIX and the KI/BioMicro computational resources
Mon October 26, 2020 2:00pm-4:30pm Jingzhi Zhu Zoom Zoom link How to install software packages yourself on computing clusters
Mon November 9, 2020 2:00pm-4:30pm Dikshant Pradhan Zoom Zoom link Public Data Repositories
Wed December 9, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 1
Wed December 16, 2020 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 2
Tuesday February 16, 2021 2pm-4:30pm Duanduan Ma zoom zoom link Introduction to UNIX and the KI/BioMicro computational resources session I
Monday February 22, 2021 2pm-4:30pm Jingzhi Zhu, Duanduan Ma zoom zoom link Introduction to UNIX and the KI/BioMicro computational resources session II
Monday March 15, 2021 2pm-4:30pm Duanduan Ma zoom zoom link Introduction of Python to biologists session I
Monday March 22, 2021 2pm-4:30pm Duanduan Ma zoom zoom link Introduction of Python to biologists session II
Monday March 29, 2021 2pm-4:30pm Duanduan Ma zoom zoom link Introduction to Biopython
Monday April 12, 2021 2pm-3pm Vincent Butty zoom zoom link A Traveler's companion to RNA-Seq interpretation session I
Monday April 26, 2021 2pm-3pm Vincent Butty zoom zoom link A Traveler's companion to RNA-Seq interpretation session II
Monday May 3, 2021 2pm-3pm Vincent Butty zoom zoom link Single Cell RNA-seq
Monday May 10, 2021 2pm-4:30pm Duanduan Ma zoom zoom link Introduction to UNIX and the KI/BioMicro computational resources session I
Monday May 17, 2021 2pm-4:30pm Jingzhi Zhu, Duanduan Ma zoom zoom link Introduction to UNIX and the KI/BioMicro computational resources session II
Monday June 7, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 1
Monday June 14, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 2
Monday September 13, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to UNIX and the KI/BioMicro computational resources
Monday September 20, 2021 2:00pm-4:30pm Jingzhi Zhu Zoom Zoom link Effective utilization of IGB computational resources - SLURM & CONDA
Monday October 11, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Python session I
Monday October 18, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Python session II
Monday October 25, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Biopython
Monday November 1, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Pandas
Monday November 8, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Matplotlib
Monday November 15, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Seaborn
Monday December 13, 2021 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Linux and the IGB computational resources
Tuesday February 8, 2022 2:00pm-4:30pm Duanduan Ma and Jingzhi Zhu Zoom Zoom link Introduction to Linux and the KI/BioMicro computational resources
Thursday March 3rd, 2022 2:00pm-3:00pm Dikshant Pradhan Zoom Zoom link Public Data Repositories
Monday March 14th, 2022 1:00pm-3:30pm Vincent Butty Zoom Zoom link RNA-Seq Design and Analysis Session I
Tuesday March 15th, 2022 1:00pm-3:30pm Vincent Butty Zoom Zoom link RNA-Seq Design and Analysis Session II
Thursday March 17th, 2022 1:00pm-3:30pm Vincent Butty Zoom Zoom link RNA-Seq Design and Analysis Session III
Monday March 28, 2022 1:00pm-3:30pm Duanduan Ma and Jingzhi Zhu Zoom Zoom link Introduction to Linux and the KI/BioMicro computational resources
Monday April 11, 2022 1:00pm-3:30pm Duanduan Ma Zoom Zoom link Introduction to R session 1
Wednesday April 13, 2022 1:00pm-3:30pm Duanduan Ma Zoom Zoom link Introduction to R session 2
Monday Apil 25th, 2022 1:00pm-3:30pm Charlie Whittaker Dikshant Pradhan Zoom Zoom link RNAseq HandsOn session 1
Wednesday Apil 27th, 2022 1:00pm-3:30pm Charlie Whittaker Dikshant Pradhan Zoom Zoom link RNAseq HandsOn session 2
Friday Apil 27th, 2022 1:00pm-3:30pm Charlie Whittaker Dikshant Pradhan Zoom Zoom link RNAseq HandsOn session 3
Monday September 19th, 2022 2:00pm-4:30pm Duanduan Ma Jingzhi Zhu Zoom Zoom link Introduction to Linux and Cluster Computing
Monday October 3rd, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session I
Tuesday October 4th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session II
Friday October 7th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Biopython
Monday October 31st, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Matplotlib
Wednesday November 2nd, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Pandas
Friday November 4th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Data processing and visualization using Python: Introduction to Seaborn
Monday November 14th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of machine learning and its applications in biology. session I
Wednesday November 16th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of machine learning and its applications in biology. session II
Monday December 5th, 2022 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Linux and Cluster Computing
Monday February 6th, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Linux and Cluster Computing
Tuesday February 21, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 1
Wednesday February 22, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to R session 2
Mon March 13, 2023 2:00pm-3:30pm Stuart Levine Zoom Zoom link Advanced Excel/Google Sheets for Biologists & Administrators
Monday April 3rd, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session I
Wednesday April 5th, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction of Python to biologists session II
Monday April 10th, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Version control with Git session I
Wednesday April 12th, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Version control with Git session II
Monday April 24th, 2023 1:00pm-3:30pm Vincent Butty Zoom Zoom link Bulk RNA-Seq Design and Analysis Session I
Wednesday April 26th, 2023 1:00pm-3:30pm Vincent Butty Zoom Zoom link Bulk RNA-Seq Design and Analysis Session II
Thursday April 27th, 2023 1:00pm-3:30pm Vincent Butty Zoom Zoom link Single cell RNA-Seq Design and Analysis Session I
Friday April 28th, 2023 1:00pm-3:30pm Vincent Butty Zoom Zoom link Single cell RNA-Seq Design and Analysis Session II
Monday May 1st, 2023 2:00pm-4:30pm Duanduan Ma Zoom Zoom link Introduction to Linux and Cluster Computing
Monday May 15th, 2023 1:00pm-3:00pm Charlie Whittaker Zoom Zoom link RNAseq HandsOn session 1
Wednesday May 17th, 2023 1:00pm-3:00pm Charlie Whittaker Zoom Zoom link RNAseq HandsOn session 2
Thursday May 18th, 2023 1:00pm-3:00pm Charlie Whittaker Zoom Zoom link RNAseq HandsOn session 3
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