Club members engage in activities related to the Bioinformatics and Genomics (BG) graduate program: Recruitment, Mentoring, Professional Development, Social outings, Retreats, Seminars and Workshops. As an interdisciplinary group, our goal is to interact with other groups at Penn State and in the broader community.
If interested in joining GenoMIX, please sign to our mailing list: L-GENOMIXfirstname.lastname@example.org
The monthly, mini-workshop materials are shared here .
Faculty Advisor: Cooduvalli Shashikant, Co-Director, Bioinformatics and Genomics Program Option
2017-2018: Wilfried Guiblet (President), Divyanshi Srivastava (Vice President), Mehreen Mughal (Secretary), Matthew Jensen (Webmaster)
2016-2017: Wilfried Guiblet (President), Monika Cechova (Vice President), Lila Rieber (Secretary), Di (Bruce) Chen (Treasurer), Matthew Jensen (Webmaster)
2015-2016: Boris Rebolledo-Jaramillo (President), Monika Cechova (Vice President), Rahulsimham Vegesna (Secretary), Theodora Maravegias (Treasurer), Zach Fuller (Webmaster), Lila Rieber (Huck-liaison)
2014-2015: Boris Rebolledo-Jaramillo (President), Samarth Rangavittal (Vice President), Yanli Wang (Secretary), Akshay Kakumanu (Treasurer), Nicholas Stoler (Webmaster)
2013-2014: Arkarachai Fungtammasan (President), Ruowang Li (Vice President), Rohit Reja (Secretary), Akshay Kakumanu (Treasurer), Nicholas Stoler (Webmaster)
2012-2013: Jihye Park (President), Nathanial Cannon (Vice President), Neerja Katiyar (Secretary), Rohit Reja (Treasurer), Ruowang Li (Webmaster)
October 16: Talk by former graduate student and GenoMIX official, Zachary Fuller on "Lessons and experiences from the journey towards a PhD and beyond"
September 22: Socials at the BG Annual Retreat
August 25, 26: Raystown Resort Welcome Weekend
March 23: Regular expressions, extremely powerful tools for quick and elegant manipulation of large text files
March 9: Socials
March 2: (Bio)Code Review
February 3: Socials with BG candidates
January 26: (Bio)code Review
January 20: Socials with BG candidates
Nov 17: Putting probablilty back into statistics with R and ggplot 2
Nov 4: (Bio)Code Review
We are starting small Tips&Tricks session including very short (~5 minutes) demonstrations on selected topics related to coding. Please volunteer to show us your hacks; these should be simple presentations including no preparation on your side. Today's topics are
"Entering world of python" by Samarth Rangavittal
"Speeding up your bio R code in simple parallelization scenario" by Monika Cechova
October 6: First (Bio)Code Reveiw
The purpose of this event is to share skills and get help with challenges related to bioinformatics. If you feel stuck in your analysis, or if you think you can provide advice for others, this event is for you. It will be less formal than our workshops and is open to people of all abilities, including people who have never coded before.
During this first session, simple ways of multitasking with python was discussed. The discussion was entertained by a staff member of the Galaxy team and small groups workied on hands on practice. Other groups had diverse research topic discussed and socializing time.
April 7: "Introduction to Data Science with Python Pandas" by Samarth Rangavittal
Looking for a powerful, yet easy-to-use alternative to R ? Or are you a beginner, trying to learn data science from scratch ? Well look no further, Python Pandas is for you. In this workshop, we will try out a dataset from the Internet Movie Database (IMDb), and write some simple Pandas code to answer questions like :
- How much money will you spend at the movie theater this holiday season ?
- Which film has the most sequels of all time ?
- In terms of Box Office records, who really wins the battle of Batman v. Superman ?
And many more questions you've secretly always wanted to ask.
- Please install anaconda for OSX, Windows or Linux
- Install Jupyter by typing 'conda install jupyter'
Files are available here
March 17: "I Spy the Genome: Calling Variants in Genomic Data" by Matthew Jensen
In this activity, we will learn about different variant callers and how to apply them to your data. We will briefly cover how variant callers work and what information is in the VCF output, as well as explore how different callers determine the quality of variants. We will also use Galaxy to learn how to use two common variant callers--Samtools and FreeBayes--and discuss which is better for your data sets.
Requirements: No programming experience or software installation is required! All of our hands-on activities will be done online using the Galaxy interface. Files are available here
February 11: "Explore Alignments (SAM/BAM) Using Pysam-powerful Python Library!" by Rahul Vegesna
We will start by explaining SAM/BAM format and the basic manipulation using samtools. Then we will dive into python and show how to extract useful information using pysam library. For our hands on part of workshop, we will use Hi-C paired-end dataset generated for embryonic stem cells. Python veterans and non-programmers are all welcome.
Requirements: None to attend, but if you want to follow along, bring a computer with a Linux/Unix environment already set up, Python and pysam installed (pip install pysam). More information can be found here
December 3: "Writing Galaxy Tools for Your Own Instance, and the World to See" by Boris Rebolledo-Jaramillo
The workshop on how to write Galaxy tools for your instance and the world, like the name suggests, has two components: local installation of your tools and how to share them. In order to test your newly created Galaxy tools, you need a working instance. So, please follow the instructions on how to install Galaxy, and make sure it works. Normally installation is quite simple. However, if you are running OSX El Capitan, you might run into an issue. I had to deactivate System Integrity Protection (SIP) in order to runGalaxy in my new computer. Check the link on how to deactivate SIP. A Galaxy tool is nothing but an XML wrapper (tool definition file) of an existing script or binary. The wrapper tells Galaxy how to implement your tool. If you already have a basic script, that you know works quickly, have a clear input and output, bring it! and we can work on it.
November 5: "Forget R, plot with Python Instead" by Lila Rieber
Tired of switching back and forth between Python and R just for the sake of plotting? We will introduce you to Matplotlib for basic plotting. Python veterans and non-programmers are all welcome.
Requirements: None to attend, but if you want to follow along, bring a computer with a Linux/Unix environment already set up, Python and R installed. If you have a Windows computer, you can use Cygwin for a Linux-like environment. To save time at the workshop, please also have the Python libraries numpy, scipy and matplotlib installed. More information and installation guides can be found here, here and here
Data and script provided here
Title of the talk: A Moving Landscape of Wildlife Genetics
Organizers: Wilfried Guiblet, Zachary Fuller and Monica Cechova
August 29, 30: 2015 Bioinformatics and Genomics Retreat
April 8: Dr. Lucilla Ohno-Machado, University of California at San Diego, Invited Speaker
Title of the talk: Genomic data sharing and privacy protection: How to combine these goals to advance research and human health.
Sep 12, 13: 2014 Bioinformatics and Genomics Retreat
April 22: Dr. Evan Eichler, University of Washington, Seattle, Invited Speaker
Title of the talk: · Resolving the Complex Organization of Human Genome using SMRT Sequencing Technology
December 13: A discussion on 'Postdoctoral Application Process' by Dr. Debashis Ghosh and Dr. Heather Hines
Interviewed by Rohit Reja
October 4, 5: 2013 Bionformatics and Genomics Retreat
September 16: Social Event
April 15: An Evening with Drs Ross Hardison and Marylyn Ritchie
Bioinformatics and Genomics - Past, Present, and Future:
We will discuss what we have achieved so far and what we need to pursue as the next generation scientists.
Feb 28: An Evening with Drs. Marcel Salathe and Shaun Mahony
How to get the most out of conferences: We will discuss how to choose good conferences to go, what to do before, during after the conferences, Do’s and Don’t’s at the conferences, and some advice from their personal experience.
Dec 7: Talks with Drs Kateryna Makova and Santhosh Girirajan
How to give a job talk: Things that are expected from a candidate. Other Do's and Don't's on how to give a talk
Nov 5: First GenoMIX Dinner
Oct 15: First GenoMIX Meeting and Social Event