General Information

BOOTCAMP INFORMATION

Organizers

Please contact the organizers for registration or other bootcamp related issues:

• Dr. Cooduvalli Shashikant, Co-Director, Bioinformatics and Genomics Program Option: css13@psu.edu
• Dana Coval-Dinant, Graduate Program Coordinator: dmc6@psu.edu

Instructors

• Dr. Naomi Altman, Professor, Dept. of Statistics
• Dr. Anton Nekrutenko, Professor, Dept. of Biochemistry and Molecular Biology
• Dr. Istvan Albert, Professor of Bioinformatics

Teaching Assistant

• Di (Bruce) Chen, TA, Graduate Student

Invited Speakers

• Dr. Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology
• Dr. Qunhua Li, Assistant Professor, Dept. of Statistics
• Dr. George Perry, Assistant Professor, Dept. of Anthropology and Biology
• Dr. James Broach, Professor, Dept. of Biochemistry and Molecular Biology, College of Medicine

Location

1. June 6-10th, 011 Life Sciences Building.
2. Breakfasts and lunches are planned. Participants are on their own for most dinners.
3. All participants need to bring a laptop.

PARTICIPANTS

Exercise: add your name to this list!

Use the information in the lectures on version control and documentation to expand this list. Fork the repository, make the changes then create a pull request.

This file is located in share/participants.md. Use the following format:

• Patricia Silveyra, Pediatrics, Penn State College of Medicine, website
• Boris Rebolledo, BMB, Penn State, website
• K Clinton, Biology, Howard University
• Anurag Verma, Bioinformatics and Genomics, Pennsylvania State University
• Nabeel Ahmed, BG, Penn State
• Aswathy Sebastian, BMB, PennState
• Huiting Zhang, Biology, Penn State
• Shefali Setia Verma, Bioinformatics and Genomics, Penn State
• Di (Bruce) Chen, Genetics, Penn State University
• Michael Campbell, Biology, Howard University
• Naomi Altman, Dept. of Statistics, Penn State
• Shefali Setia Verma, Bioinformatics and Genomics, Penn State
• Istvan Albert, Biochemistry and Molecular Biology, Penn State
• Zhenzhen Yang, Biology, Penn State
• Lila Rieber, Biochemistry and Molecular Biology, Penn State
• Wanyan Wang, Plant Biology, Penn State
• Lihua Wu Plant Biology Program, Penn State University
• Bo Zhang, Biochemistry&Molecular Biology, Penn State University, bzhang2@psu.edu.edu
• Di Wu, BG program, Penn State
• njlaa, Biology, Howard
• Binglan Li, Bioinformatics & Genomics, Pennsylvania State University
• Yong Jung, Bioinformatics and Genomics, Penn State University
• Anna Basile, Biochemistry, Penn State University
• Christopher Cross, Anatomy, Howard University
• Cody Molnar, Biochemistry and Molecular Biology, Penn State Hershey
• Matthew Jensen, Bioinformatics and Genomics, Penn State University
• Michael C. Campbell, Biology, Howard University
• Julie White, Anthropology, Penn State
• Yong Jung, Bioinformatics and Genomics, Penn State University
• Viridiana Avila, Biology Department, Pennsylvania State University
• Divyanshi Srivastava, Bioinformatics and Genomics, Penn State University
• Latifa Jackson, National Human Genome Center and Pediatrics, Howard University
• Naomi Yamada, Bioinformatics and Genomics, Penn State University
• Di (Bruce) Chen, Genetics, Penn State University (dxc385@psu.edu)
• Lina Castano-Duque, Plant Biology, Penn State

SUGGESTIONS

What should be cover during day 5:

• Making Galaxy tools.
• How to run code in parallel.
• Show example of a realtime project in Git/Python.
• Best programming practices in general.
• Run a local environment of Galaxy/Build Galaxy tools.
• Comparison of creating reports with R markdown vs Jupyter.
• Using Plotly and Jupyter to generate interactive plots.
• How to choose simple statistical tests.
• Create a step-by-step guide to generate a repository in github that can be shared in a paper or grant application
• Show us how to improve figures using plot and related functions in gplot or gplot2 of R, for example, changing label, or legend of many kinds of plots - boxplot, clustering plots, scatterplot, and so on

Suggestions go here

• Making Galaxy tools
• Plotly to interactive plots using Jupyter

HOW TO GENERATE THE SITE

First of all note that you don't actually need to fully generate this site yourself during the bootcamp. These instructions are here just to explain the process. But even if you don't generate the site itself you may still contribute to it via the GitHub web interface or after cloning locally.

The website is generated from the files in the web directory of the bootcamp-central repository via the pyblue python package. For it work you would need to have both Python and the pip package manager installed.

Clone the repository:

git clone https://github.com/biostars/bootcamp-central

Install pyblue from last year:

pip install pyblue==2016.6.2

You can now view the site as HTML with:

cd bootcamp-central

the default Makefile action is to run the server:

make

or

pyblue -r web/2016

This will start a web server on your computer and you can use the browser to view the contents of the site. This is used while developing the site.

http://localhost:8080

To generate a published version of the site add the -o parameter with a directory name that is meant to store the output destination

pyblue -r web/2016 -o /final/directory