BOSC Vienna, Austria July 20, 2007 Kam D. Dahlquist Department of Biology John David N. Dionisio Department of Electrical Engineering & Computer Science Loyola Marymount University An Open Source Framework for Teaching Bioinformatics

Outline Motivation Open source culture Implementation --Computer science curriculum --Bioinformatics course

Motivation

Open source culture

Implementation

--Computer science curriculum

--Bioinformatics course

Scientific Computing and the Digital Divide Wilson GV (2006) Where’s the real bottleneck in scientific computing? American Scientist 94:5–6. Scientists who come to computer science after being trained in a different primary discipline often have to rediscover, relearn, or keep up with work in the computer science and software development realms in order to get the most out of their work. This causses unecessary and unknowing repetitions of past discoveries and errors. Tools or paradigms that are out-of-date in computer science and software engineering remain in place. At worst, software flaws slow or impede research. Baxter SM, Day SW, Fetrow JS, and Reisinger SJ (2006) Scientific software development is not an oxymoron. PLoS Computational Biology 2:e87.

The Disconnect Between Undergraduate Computer Science Training and Expectations and Skill Sets Required for Industry and Research Undergraduate Training Industry Expectation Work alone Work in a team “ Toy” programs and algorithms Large, modular project Throwaway code Code longevity (for better or worse)

inroads – The SIGCSE Bulletin, Volume 39, Number 2, 2007 June, pp. 70-74 http://recourse.cs.lmu.edu/

Official Open Source Definition (version 1.9) Free redistribution Source code Derived works Integrity of the author’s source code No discrimination against persons or groups No discrimination against fields of endeavor Distribution of license License must not be specific to a product License must not restrict other software License must be technology-neutral

Open Source Values Source code is available, modifiable, and long-lived Accountability implies community --explicit “paper trail” for how a particular program changes over time --communication and answerability Responsibilities accompany rights --explicit consideration of the license --giving credit where it is due --appropriate access to software, documentation, and communities --acknowledging security, privacy, legal issues

Source code is available, modifiable, and long-lived

Accountability implies community

--explicit “paper trail” for how a particular program

changes over time

--communication and answerability

Responsibilities accompany rights

--explicit consideration of the license

--giving credit where it is due

--appropriate access to software, documentation, and

communities

--acknowledging security, privacy, legal issues

Open Source Teaching Framework Source Code: All code resides in a centralized, public repository As much as possible, everyone’s code is visible to everyone else for code review or team fixing No code is thrown away, it remains available to future “ generations”

Source Code:

All code resides in a centralized, public repository

As much as possible, everyone’s code is visible to

everyone else for code review or team fixing

No code is thrown away, it remains available to future

“ generations”

Open Source Teaching Framework Source Code: All code resides in a centralized, public repository As much as possible, everyone’s code is visible to everyone else for code review or team fixing No code is thrown away, it remains available to future “ generations” Quality & Community: Documentation, inline and online Automated tests Constructive code review, beyond “does it work?” Long-term projects release early, release often Form collaborative communities among faculty, students, classes, and projects

Source Code:

All code resides in a centralized, public repository

As much as possible, everyone’s code is visible to

everyone else for code review or team fixing

No code is thrown away, it remains available to future

“ generations”

Quality & Community:

Documentation, inline and online

Automated tests

Constructive code review, beyond “does it work?”

Long-term projects release early, release often

Form collaborative communities among faculty,

students, classes, and projects

Progression through Computer Science Curriculum Sample code bazaar --the creation and maintenance of live, organized, searchable, student accessible sample code libraries --students check out, modify, and check in code Test infection (Erich Gamma) --test suite vs. implementation matrix Life cycle of code --as juniors and seniors, students revisit code written the first year --direct experience with need for documentation Release early, release often --applies to both students and faculty

Sample code bazaar

--the creation and maintenance of live, organized, searchable,

student accessible sample code libraries

--students check out, modify, and check in code

Test infection (Erich Gamma)

--test suite vs. implementation matrix

Life cycle of code

--as juniors and seniors, students revisit code written the first

year

--direct experience with need for documentation

Release early, release often

--applies to both students and faculty

“ CourseForge” A Hardware + Software Infrastructure for Supporting the Teaching Framework Certain teaching elements are impractical without some degree of automation Support platform for management of student work --revision control --test frameworks --communication --issue tracking Derived from open source software, delivered as open source software — the system will interoperate with existing open source tools

Certain teaching elements are impractical without

some degree of automation

Support platform for management of student work

--revision control

--test frameworks

--communication

--issue tracking

Derived from open source software, delivered as

open source software — the system will interoperate

with existing open source tools

CMSI 698: Special Studies in Bioinformatics Team-taught by a biologist and a computer scientist

Team-taught by a biologist and a computer scientist

CMSI 698: Special Studies in Bioinformatics Team-taught by a biologist and a computer scientist Enrollment in Spring 2006: -- eight students from Master’s degree program in Computer Science -- several coming from aerospace industry -- none with more than college-level introductory biology

Team-taught by a biologist and a computer scientist

Enrollment in Spring 2006:

-- eight students from Master’s degree

program in Computer Science

-- several coming from aerospace industry

-- none with more than college-level introductory biology

CMSI 698: Special Studies in Bioinformatics Team-taught by a biologist and a computer scientist Enrollment in Spring 2006: -- eight students from Master’s degree program in Computer Science -- several coming from aerospace industry -- none with more than college-level introductory biology Project-based class began development of XMLPipeDB

Team-taught by a biologist and a computer scientist

Enrollment in Spring 2006:

-- eight students from Master’s degree

program in Computer Science

-- several coming from aerospace industry

-- none with more than college-level introductory biology

Project-based class began development of XMLPipeDB

CMSI 698: Special Studies in Bioinformatics Team-taught by a biologist and a computer scientist Enrollment in Spring 2006: -- eight students from Master’s degree program in Computer Science -- several coming from aerospace industry -- none with more than college-level introductory biology Project-based class began development of XMLPipeDB XMLPipeDB development continued by four students in summer session course entitled Open Source Software Development Workshop

Team-taught by a biologist and a computer scientist

Enrollment in Spring 2006:

-- eight students from Master’s degree

program in Computer Science

-- several coming from aerospace industry

-- none with more than college-level introductory biology

Project-based class began development of XMLPipeDB

XMLPipeDB development continued by four students

in summer session course entitled Open Source Software

Development Workshop

CMSI 698: Special Studies in Bioinformatics Team-taught by a biologist and a computer scientist Enrollment in Spring 2006: -- eight students from Master’s degree program in Computer Science -- several coming from aerospace industry -- none with more than college-level introductory biology Project-based class began development of XMLPipeDB --authentic bioinformatics problem to solve XMLPipeDB development continued by four students in summer session course entitled Open Source Software Development Workshop One student continued development for Master’s thesis

Team-taught by a biologist and a computer scientist

Enrollment in Spring 2006:

-- eight students from Master’s degree

program in Computer Science

-- several coming from aerospace industry

-- none with more than college-level introductory biology

Project-based class began development of XMLPipeDB

--authentic bioinformatics problem to solve

XMLPipeDB development continued by four students

in summer session course entitled Open Source Software

Development Workshop

One student continued development for Master’s thesis

XMLPipeDB Project Management: Lessons Learned Students on the project had varying levels of maturity, knowledge, and skill coming into the project -- some naturally took on a leadership role -- some hung back or did the minimum required to get by

Students on the project had varying levels of maturity,

knowledge, and skill coming into the project

-- some naturally took on a leadership role

-- some hung back or did the minimum required to get by

XMLPipeDB Project Management: Lessons Learned Students on the project had varying levels of maturity, knowledge, and skill coming into the project -- some naturally took on a leadership role -- some hung back or did the minimum required to get by Needed to increase communication and sense of team -- students preferred to interact with faculty for questions, rather than each other -- bug trackers and developer’s forum used only sporadically -- implemented weekly reports on Wiki to increase accountability

Students on the project had varying levels of maturity,

knowledge, and skill coming into the project

-- some naturally took on a leadership role

-- some hung back or did the minimum required to get by

Needed to increase communication and sense of team

-- students preferred to interact with faculty for questions,

rather than each other

-- bug trackers and developer’s forum used only sporadically

-- implemented weekly reports on Wiki to increase accountability

XMLPipeDB Project Management: Lessons Learned Students on the project had varying levels of maturity, knowledge, and skill coming into the project -- some naturally took on a leadership role -- some hung back or did the minimum required to get by Needed to increase communication and sense of team -- students preferred to interact with faculty for questions, rather than each other -- bug trackers and developer’s forum used only sporadically -- implemented weekly reports on Wiki to increase accountability [SourceForge servers were frequently down during class]

Students on the project had varying levels of maturity,

knowledge, and skill coming into the project

-- some naturally took on a leadership role

-- some hung back or did the minimum required to get by

Needed to increase communication and sense of team

-- students preferred to interact with faculty for questions,

rather than each other

-- bug trackers and developer’s forum used only sporadically

-- implemented weekly reports on Wiki to increase accountability

[SourceForge servers were frequently down during class]

XMLPipeDB Project Management: Lessons Learned Students on the project had varying levels of maturity, knowledge, and skill coming into the project -- some naturally took on a leadership role -- some hung back or did the minimum required to get by Needed to increase communication and sense of team -- students preferred to interact with faculty for questions, rather than each other -- bug trackers and developer’s forum used only sporadically -- implemented weekly reports on Wiki to increase accountability [SourceForge servers were frequently down during class] 6 months from conception to product

Students on the project had varying levels of maturity,

knowledge, and skill coming into the project

-- some naturally took on a leadership role

-- some hung back or did the minimum required to get by

Needed to increase communication and sense of team

-- students preferred to interact with faculty for questions,

rather than each other

-- bug trackers and developer’s forum used only sporadically

-- implemented weekly reports on Wiki to increase accountability

[SourceForge servers were frequently down during class]

6 months from conception to product

XMLPipeDB Project Management: Lessons Learned Students on the project had varying levels of maturity, knowledge, and skill coming into the project -- some naturally took on a leadership role -- some hung back or did the minimum required to get by Needed to increase communication and sense of team -- students preferred to interact with faculty for questions, rather than each other -- bug trackers and developer’s forum used only sporadically -- implemented weekly reports on Wiki to increase accountability [SourceForge servers were frequently down during class] 6 months from conception to product Even the weakest student contributed useable code

Students on the project had varying levels of maturity,

knowledge, and skill coming into the project

-- some naturally took on a leadership role

-- some hung back or did the minimum required to get by

Needed to increase communication and sense of team

-- students preferred to interact with faculty for questions,

rather than each other

-- bug trackers and developer’s forum used only sporadically

-- implemented weekly reports on Wiki to increase accountability

[SourceForge servers were frequently down during class]

6 months from conception to product

Even the weakest student contributed useable code

Take-home Messages Catch them early Making open source values and software development best practices explicit will produce better software and better computer scientists

Catch them early

Making open source values and software development best practices explicit will produce better software and better computer scientists

XSD-to-DB Adam Carasso Jeffrey Nicholas Scott Spicer XMLPipeDBUtils David Hoffman Babak Naffas Jeffrey Nicholas Ryan Nakamoto UniProtDB Joe Boyle Joey Barrett GODB Scott Spicer Roberto Ruiz GenMAPP Builder Joey Barrett Jeffrey Nicholas Scott Spicer Special Thanks GenMAPP.org Development Group Caskey L. Dickson, Wesley T. Citti NSF CCLI Program (http://recourse.cs.lmu.edu) http://xmlpipedb.cs.lmu.edu LMU Bioinformatics Group Kam D. Dahlquist http://myweb.lmu.edu/kdahqui [email_address] John David N. Dionisio http://myweb.lmu.edu/dondi [email_address]