The Huck Institutes of the Life Sciences

GenoMIX: Graduate Student Organization for Genomics interest

A forum for graduate students whose research is related to bioinformatics and genomics

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-GENOMIX-subscribe-request@lists.psu.edu

Follow us on facebook  and twitter @PSU_GenoMIX. 

The monthly, mini-workshop materials are shared here . 

Officers

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)

 

Activities 

                                                                                                           2017                                             

                                                                                                                                                       

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

 

2016

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.

Before coming

- 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

 

2015

 

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 herehere and here

Data and script provided here 

 

October 13:  Dr. Stephen O' Brien, St Petersburg State University, Russia,  Invited Speaker in Distinguished Lecture Series

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

Organized by Akshay KakumanuRuowang LiNaomi YamadaIsrael Rivera Colon, and Di Wu

 

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.

Organized by: Lila RieberRahul Vegesna and Tao Yang

 

2014

 

Sep 12, 13: 2014 Bioinformatics and Genomics Retreat

Organized by Wilfried GuibletRahulsimham VegesnaRohit Reja and Yanli Wang

 

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

Organized by Arkarachai FungtammasanQingyu Wang and Ruowang Li

 

February 3: Student talks by Chris Morrissey and Bongsoo Park

 

2013

 

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

Organized by Boris Rebolledo Jaramillo, Juan Antonio Raygoza Garay, Yang Liu

 

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.

 

2012

 

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