#+title: Building community developed open source infrastructure to support large-scale biology
#+author: Brad Chapman \\ Bioinformatics Core, Harvard Chan School \\ https://bcb.io \\ http://j.mp/bcbiolinks
#+date: 23 September 2015

#+OPTIONS: toc:nil H:2

#+startup: beamer
#+LaTeX_CLASS: beamer
#+latex_header: \usepackage{url}
#+latex_header: \usepackage{hyperref}
#+latex_header: \hypersetup{colorlinks=true}
#+BEAMER_THEME: default
#+BEAMER_COLOR_THEME: seahorse
#+BEAMER_INNER_THEME: rectangles

* My background

** Overview

\Large
- My background
- Research scientist at a core facility
- The open source bioinformatics community
- Why you want to work as a research scientist
- How to prepare yourself

** Undergrad Michigan State (Ecology)

#+ATTR_LATEX: :width .75\textwidth
[[./images7/Austrian_pine.jpg]]

\tiny https://en.wikipedia.org/wiki/Pinus_nigra

** Undergrad Michigan State (Plant transformation)

#+BEGIN_CENTER
#+ATTR_LATEX: :width .5\textwidth
[[./images7/Genegun.jpg]]
#+END_CENTER

\tiny https://en.wikipedia.org/wiki/Gene_gun

** PhD University of Georgia (Duplicate evolution)

[[./images6/uga_paper.png]]

** Synthetic biology startup (2004-2009)

#+BEGIN_CENTER
#+ATTR_LATEX: :width .5\textwidth
[[./images6/codon_devices.png]]
#+END_CENTER

\vspace{1.5cm}

\scriptsize
http://www.synthesis.cc/2009/04/on-the-demise-of-condon-devices.html
\normalsize

** Bioinformatics core -- Harvard Chan School

#+BEGIN_CENTER
#+ATTR_LATEX: :width .6\textwidth
[[./images7/harvard_chan.png]]

\vspace{1cm}

http://bioinformatics.sph.harvard.edu/
#+END_CENTER

* Work

** Overview

\Large
- My background
- Research scientist at a core facility
- The open source bioinformatics community
- Why you want to work as a research scientist
- How to prepare yourself

** Practical

\Large
- Work in a support core
- Consulting
- Team of 8 researchers \\
  \normalsize http://bioinformatics.sph.harvard.edu/people/
\Large
- Specialize, but also overlap
- Research scientists

** 
#+ATTR_LATEX: :width 1.1\textwidth
[[./images7/careers.jpg]]

\scriptsize http://www.sciencedirect.com/science/article/pii/S0968000414001728

** Who we work with?

\Large
- Academic Researchers: Harvard Stem Cell Institute, Harvard Medical School,
  Harvard NeuroDiscovery Center, Massachusetts General Hospital
- Large consortium projects: Cure Alzheimer's, Global Alliance for Genomic Health
- Industry: AstraZeneca, Biogen, Merck
- Startups

** Day to day work

\Large
- Collaboration with researchers
- Data analysis
- Teaching and training
- Large scale infrastructure development

** Biological questions

\Large

- Alzheimer's -- large populations of affected families
- Cancer treatment -- detection of driver mutations, relapse after treatment
- HIV -- detection of low frequency drug resistant sub-populations

** Human whole genome sequencing

[[./images5/human_genome.png]]

\footnotesize
http://ensembl.org/Homo_sapiens/Location/Genome
\normalsize

** High throughput sequencing

[[./images5/reads.png]]

** Variant calling

[[./images5/SNV_calling.png]]

\footnotesize
http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data
\normalsize

** Scale: exome to whole genome

[[./images5/exome_proportion.png]]

\footnotesize
https://www.flickr.com/photos/119980645@N06/
\normalsize


* Open source bioinformatics

** Overview

\Large
- My background
- Research scientist at a core facility
- The open source bioinformatics community
- Why you want to work as a research scientist
- How to prepare yourself

** Large scale infrastructure development

\Large
- Find shared problems
- Community developed analyses
- Validation
- Scaling
- Supporting a community of users
\normalsize

** White box software

[[./images5/clear_box.jpg]]

** Overview

#+ATTR_LATEX: :width 1.0\textwidth
[[./images3/bcbio_nextgen_highlevel.png]]

\vspace{1cm}
https://github.com/chapmanb/bcbio-nextgen

** Provides

\Large
- Community -- collected set of expertise
- Tool integration
- Validation -- outputs + automated evaluation
- Scaling
- Installation of tools and data
\normalsize

** Solution

#+BEGIN_CENTER
#+ATTR_LATEX: :width .5\textwidth
[[./images/community.png]]
#+END_CENTER

\scriptsize
[[http://www.amazon.com/Community-Structure-Belonging-Peter-Block/dp/1605092770]]
\normalsize

** Community: contribution

[[./images5/bcbio_github.png]]

[[https://github.com/chapmanb/bcbio-nextgen]]

** Community: documentation

[[./images/community-docs.png]]

[[https://bcbio-nextgen.readthedocs.org]]

** Sustainability

\Large
A piece of software is being sustained if people are using it, fixing it, and
improving it rather than replacing it.

\vspace{0.5cm}

\normalsize
http://software-carpentry.org/blog/2014/08/sustainability.html



* Why research scientist

** Overview

\Large
- My background
- Research scientist at a core facility
- The open source bioinformatics community
- Why you want to work as a research scientist
- How to prepare yourself

** Research scientist as a career -- pros

\Large
- Wide range of projects
- Collaboration
- Respected
- Help others
- Grow and learn
\normalsize

** Open source communities -- pros

\Large
- Work on problems with impact
- Large set of peers
- Fortuitous interactions
- Transferable skills

** Research scientist -- cons

\Large
- Less control over overall biological questions
- Juggle more simultaneous projects

* Training

** Overview

\Large
- My background
- Research scientist at a core facility
- The open source bioinformatics community
- Why you want to work as a research scientist
- How to prepare yourself

** Learning good practices

[[./images6/software-carpentry.png]]

\vspace{0.3cm}

[[./images6/mozilla-science-lab.png]]

\vspace{0.3cm}

\Large
http://software-carpentry.org \\
\vspace{0.1cm}
http://mozillascience.org
\normalsize

** Revision control

#+ATTR_LATEX: :width 0.6\textwidth
[[./images6/github.png]]

\vspace{0.3cm}

#+ATTR_LATEX: :width 0.6\textwidth
[[./images6/bitbucket-logo.png]]

\vspace{0.3cm}

\Large
http://github.com \\
\vspace{0.1cm}
https://bitbucket.org
\normalsize

** Reproducible environments

[[./images6/ipython.png]]

\vspace{0.3cm}

#+ATTR_LATEX: :width 0.6\textwidth
[[./images6/rstudio.png]]

\vspace{0.3cm}

\Large
http://jupyter.org/ \\
http://ipython.org \\
\vspace{0.1cm}
http://www.rstudio.com/
\normalsize

** Good practices = good science

#+BEGIN_CENTER
#+ATTR_LATEX: :width 0.4\textwidth
[[./images6/biodata_skills.jpg]]
#+END_CENTER

http://shop.oreilly.com/product/0636920030157.do

** Open Source Communities

#+ATTR_LATEX: :width 0.3\textwidth
[[./images6/obf.jpg]]

\vspace{0.2cm}

#+ATTR_LATEX: :width 0.5\textwidth
[[./images6/galaxy.png]]

\vspace{0.3cm}
http://www.open-bio.org \\
\vspace{0.05cm}
http://www.open-bio.org/wiki/BOSC_2014 \\
\vspace{0.05cm}
http://usegalaxy.org \\
\vspace{0.05cm}
https://wiki.galaxyproject.org/Events/GCC2014
\normalsize


** Summary

\Large
- Bioinformatics core at Harvard Chan School
- Collaborative research work
- Open source community
- Contribute to public health research

\Large
\vspace{1cm}
https://bcb.io \\
\vspace{.5cm}
https://j.mp/bcbiolinks
\normalsize
