Calendar & Events

 

Summer 2020

ISU/OSU meetings

  • Will be in Microsoft Teams, invite will go to all OSU faculty, with notes on who is presenting each day
  • Regular times will be Tuesdays and Wednesdays from 1-4pm, with presentation 1-2, 2-3 break, presentation 3-4.  Break will be used for student questions, working on activities, etc.
  • Each OSU faculty member is "on duty" for a two week chunk, which will be four afternoon slots (Tue/Wed 1-4pm).  Plan for two sessions of presentations/workshops, which will likely take three days for the students to digest, and hold the fourth day for ISU faculty consults.

Getting Started

For those who will participate/attend the summer 2020 workshops, your steps to get started are ...

  • Sign up for a free account at gitlab.com and send your login to jkinne@indstate.edu to be added to a gitlab repository where files for the summer workshops will be kept.
  • Install the git client for your computer if you don't already have one installed (Linux and Mac OS normally have git already installed, Windows normally not).  Later on, see the Gitlab Getting Started for more about Git.
  • Follow the instructions at R Programming Getting Started to install the following on your computer: R, Rstudio.
  • Make sure you have either a current version of Chrome or Edge installed, or install the Microsoft Teams application (scroll down to see download link).
  • Follow this link to request to be added to the Microsoft Team where online meetings will be held, and recordings will be kept.
  • Once you have been added to the Microsoft Team, use the "Troubleshooting and status" channel in the team to post questions about current tasks, post status on completing tasks, etc.  Some of these we can work through in the chat, others we will work through during our meetings or one on one calls.

Week 1, May 18-22

  • Jeff Kinne - R, Gitlab, Rmd
    • Assignment 0 - follow the above Getting Started Steps.
    • Assignment 1 - follow along the R Programming Getting Started and start reading through the suggested reading.
    • Assignment 2a - go to https://gitlab.com/krcoombes/osu-isu-workshop, click "master" near the middle and change to "jeff-kinne", then click on the download icon on the right side of the screen to download a zip file of the project.  Unzip the file and see what you have.  Look in the directory code/R-basics/
    • Assignment 2b - or, do the following in your terminal to get the files ...
      Use the cd command to browse to the directory where you want the project files to be.
      git clone https://gitlab.com/krcoombes/osu-isu-workshop.git
      cd osu-isu-workshop
      git checkout jeff-kinne
      git pull https://gitlab.com/krcoombes/osu-isu-workshop.git jeff-kinne
      cd code
      cd R-basics
      And there should be files in that directory.  Start by looking at Readme.md
  • Mark Inlow - statistics
  • Jeff Kinne, OSU faculty - returning students choosing OSU faculty member to work with

Weeks 2-3, May 26/27, June 2/3

  • Kevin Coombes, HouseKeeper
    • Pre-requisites: R installed, gitlab.com account, send gitlab.com account to Kevin and Jeff so you can be added to two gitlab projects (HouseKeepeR and OSU-ISU-Workshop).
  • Draft of other OSU workshops ready for Jeff to look over, so if something would be useful for ISU summer projects

Weeks 4-5, June 9/10, 16/17

  • Yan Zhang, RNAseq, pathway analysis
  • Friday June 12 - Fourth statistics session with Mark Inlow, 1-2pm and 3-4pm.  Meeting on zoom, link to the meeting sent to the BD4ISU email list.

Weeks 6-7, June 23/24, June 30/July 1

  • Lijun Cheng, precision medicine, multi-omics data, clustering

Weeks 8-9, July 7/8, 14/15

  • Qin Ma, single cell RNAseq analysis, public packages and in-house web server, clustering

Week 10, July 20-24

  • ISU students working on posters
  • Virtual poster presentations, likely July 21/22

Spring 2020

Participants met with Dr. Jeff Kinne twice weekly for CS 459 on Monday 9-9:50 and Thursday 3:30-4:20. The course website is - http://cs.indstate.edu/~jkinne/cs459-bd4isu-s2019/

Fall 2019

Participants met weekly with Dr. Rusty Gonser  for Bio 491-"Genetic Survey for Bioinformatics".

BD4ISU students participated in the Fall Exposium.  

Summer 2019

The summer 2019 workshop schedule is below. 

Date Time(s) Campus Room What
May 20   OSU   Summer internship at OSU begins for BD4ISU first cohort
May 20 -
May 21
8am-5pm,
8am-noon
ISU Dede III Research Integrity Workshop - organized by the Office of Sponsored Programs, required for BD4ISU students working at ISU in the summer
May 22   ISU   Summer research at ISU begins
May 22-24 9am - noon ISU Root Hall
A-017
R Programming - workshop by Jeff Kinne (Associate Professor, Dept Math & CS)
May 24 -
July 26
11:45am -
1:30pm
ISU Science
basement
Each Friday from May 24 - July 26, research presentations with SURE from noon-1:30pm, with lunch provided at 11:45am.
May 28 -
May 29
9am-noon ISU Root Hall
basement
Statistics - Workshop/tutorial by Mark Inlow (Assistant Professor, Dept Math & CS)
May 30 -
May 31
9am-4pm,
9am-noon
ISU Root Hall
A-017
Metabolite-Gene Integration Tools - Workshop by Ewy Mathe (Assistant Professor, Dept Biomedical Informatics, The Ohio State University)
June 4 -
June 5
9am-noon ISU Root Hall
basement
Statistics - Workshop/tutorial by Mark Inlow (Assistant Professor, Dept Math & CS)
June 6 -
June 7
9am-4pm,
9am-noon
ISU Root Hall
A-017
Bioinformatics in RNA-seq Data - Workshop by Yan Zhang (Assistant Professor, Dept Biomedical Informatics, The Ohio State University)
June 9 -
June 11
  OSU The Blackwell ICIBM conference (International Conference on Intelligent Biology and Medicine) at OSU
June 20 -
June 21
9am-4pm,
9am-noon
ISU Root Hall
A-017
Collaborative/Reproducible Bioinformatics - Workshop by Kevin Coombes (Professor, Dept Biomedical Informatics, The Ohio State University)
June 20 -
June 21
9am-4pm,
9am-noon
ISU Root Hall
A-017
Collaborative/Reproducible Bioinformatics - Workshop by Kevin Coombes (Professor, Dept Biomedical Informatics, The Ohio State University)
July 3 11-noon ISU Root Hall
A-017
Metabolites and Microbiome in the Mouse Colon - Presentation by Cynthia Ramazani (Biology major, BD4ISU participant)
July 3 1:30-3pm ISU Root Hall
A-017
R Programming Refresher - workshop by Jeff Kinne (Associate Professor, Dept Math & CS)
July 10 2-3pm ISU Root Hall
A-017
Cytogenetic Analysis of B-Cell Malignancies - Presentation by Dwayne Tally (Computer Science major, BD4ISU participant)
July 11-
July 12
9am-4pm
9am-11:30am
ISU Root Hall
A-017
Bioinformatics and Machine Learning - Workshop by Lijun Cheng (Assistant Professor, Dept Biomedical Informatics, The Ohio State University)
July 14 -
July 20
  ISU TBA Summer honors for high school students, BD4ISU assist in hosting. Classes run M-F 8:30am-3:30pm.
July 17 -
July 18
10-noon ISU S 297 Bioinformatics refresher - by Naureen Aslam (PhD student, Department of Biology, ISU)
July 27   OSU   Summer internship at OSU ends for BD4ISU first cohort
August 1 TBA ISU TBA Poster session for BD4ISU at ISU

Spring 2019

Key dates

Date Where What
March 30 Indianapolis Indiana Academy of Sciences - Annual Meeting
March 31 - April 1 OSU BD4ISU students and facult meet OSU faculty, complete paperwork needed for summer research internship
Tuesdays 4-5pm, Fridays 4-5pm ISU Root Hall A-017 CS 459 Programming in Bioinformatics, taught by Dr. Jeff Kinne

 

Summer 2018

  • Research Integrity Symposium

    • May 22, 8am-5pm - in Science 214.
    • Organizers - Andrew-Sheppard Smith (Office of Sponsored Programs, Director), Rusty Gonser (Professor, Dept Biology, Director of TCGA)
  • An Introduction to Web-based Bioinformatics
    • May 23 9am-4pm, May 24 9am-4pm, May 25 9am-11:30am - in University Hall 008R
    • Presenter – Jennifer Smith, microbiology
  • R Programming and Unix/Linux
    • May 29 9am-noon, May 30 9am-noon, May 31 9am-noon - in Root Hall A-017
    • Presenter – Jeff Kinne, Associate Prof, Dept of Math & Computer Science, Associate Director of TCGA
  • Statistics
    • June 4-8, 9-10:30am each day in Root Hall basement
    • Presenter – Liz Brown, Professor and Chairperson, Dept Math & Computer Science
  • Collaborative Bioinformatics
    • June 14 9am-4pm, June 15 9am-11:30am - in University Hall 008R
    • Presenter – Kevin Coombes, Professor, Dept Biomedical Informatics, The Ohio State University
  • Bioinformatics in RNA-seq Data
    • June 21 9am-4pm, June 22 9am-11:30am - in University Hall 008R
    • Presenter – Guy Brock, Research Assoc Prof, Dept Biomedical Informatics, The Ohio State University
  • Students work with research advisors
    • Weeks of June 25-29 and July 2-6
    • No workshopes, students have more time to work on their research projects
  • Bioinformatics and Machine Learning
    • July 12 9am-4pm, July 13 9am-11:30am - in University Hall 008R
    • Presenter – Fuhai Li, Assistant Professor, Dept Biomedical Informatics, The Ohio State University
  • Wet Lab Training
    • Integrated into TCGA Summer Honors course for BD4ISU-supported students - July 16-20
    • Presenter – Catherine Steding, Assistant Professor, Dept Biology
  • Shiny Apps and Metabolite-Gene Integration Tools
    • July 26 9am-4pm, July 27 9am-11:30am - in University Hall 008R
    • Presenter – Ewy Mathe, Assistant Professor, Dept Biomedical Informatics, The Ohio State University
  • Poster Preparation and Symposium
    • Week of July 30-August 3

More detailed information on the summer 2018 workshops is contained in the following - BD4ISU Summer Workshop 2018 Schedule.

Video lectures, slides, etc. are posted in a Blackboard site for the project. If you are an ISU student, faculty, or staff please write to us to ask to be added to the course.