BOSC2014_schedule.tex

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\lhead{{\Large \textbf{Bioinformatics Open Source Conference (BOSC) 2014}}\vspace{1mm}\\A Special Interest Group (SIG) meeting at ISMB 2014, Boston, MA, USA}
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\noindent
BOSC is organised by the Open Bioinformatics Foundation
(OBF, \href{http://www.open-bio.org}{www.open-bio.org}),
one of the ISCB Communities of Special Interest (COSIs).
The OBF is a non-profit group that promotes the practice and
philosophy of Open Source software development and Open Science in
the biological research community.

%\section*{Bioinformatics Open Source Conference (BOSC)}
\subsection*{BOSC Schedule - Day One - Friday, 11 July 2014}

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\begin{tabular}{|p{2.0cm}|p{10cm}|p{3.3cm}|}
\hline
Time & Title & Author/Notes \\
\hline
\textbf{7:30-9:00} & \textbf{Registration} &\\
\hline
9:00-9:15 & Introduction and Welcome &\\
9:15-10:15 & \textbf{Keynote}: A History of Bioinformatics (in the Year 2039) & C. Titus Brown\\
\hline
\textbf{10:15-10:45} & \textbf{Coffee Break} &\\
\hline
\textbf{10:45-12:30} & \textbf{\textit{Session: Genome-scale Data and Beyond}} & Chair: Chris Fields\\
10:45-11:03 & ADAM: Fast, Scalable Genomic Analysis & Frank Austin Nothaft\\
11:03-11:21 & A Framework for Benchmarking RNA-seq Pipelines & Rory Kirchner\\
11:21-11:39 & New Frontiers of Genome Assembly with SPAdes 3.1 & Andrey Prjibelski\\
11:39-11:57 & SigSeeker: An Ensemble for Analysis of Epigenetic Data & Jens Lichtenberg\\
11:57-12:15 & Galaxy as an Extensible Job Execution Platform & John Chilton\\
\hline
12:15-12:30 & Open Bioinformatics Foundation (OBF) Update & Hilmar Lapp\\
\hline
\textbf{12:30-13:30} & \textbf{Lunch} & (Lunch and poster\\
\textbf{13:00-14:00} & \textbf{Poster Session and Birds of a Feather (BOFs)} & session overlap)\\
\hline
\textbf{14:00-15:30} & \textbf{\textit{Session: Visualization}} & Chair: Rob Davey\\
14:00-14:18 & WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution & Anthony Santella\\
14:18-14:36 & BioJS: an Open Source Standard for Biological Visualisation & Manuel Corpas\\
14:36-14:54 & Biodalliance: a Fast, Extensible Genome Browser & Thomas Down\\
14:54-15:12 & TGAC Browser: Visualisation Solutions for Big Data in the Genomic Era & Anil S. Thanki\\
15:12-15:30 & Explore, Analyze, and Share Genomic Data Using Integrated Genome Browser & Ann Loraine\\
\hline
\textbf{15:30-16:00} & \textbf{Coffee Break} &\\
\hline
\textbf{16:00-17:00} & \textbf{\textit{Session: Project Updates}} & Chair: Peter Cock\\
16:00-16:12 & BioMart 0.9 -- Introducing Tools for Data Analysis and Visualisation & Luca Pandini\\
16:12-16:24 & Biocaml: The OCaml Bioinformatics Library & Ashish Agarwal\\
16:24-16:36 & BioRuby and Distributed Development & Pjotr Prins\\
16:36-16:48 & Biopython Project Update & Wibowo Arindrarto\\
16:48-17:00 & Shared Bioinformatics Database Within Unipro UGENE & Ivan Protsyuk\\
\hline
\textbf{17:00-17:30} & \textbf{\textit{Session: Lightning Talks}} & Chair: Peter Cock\\
17:00-17:05 & Fostering the Next Generation of Data-driven Open Science with R & Karthik Ram\\
17:07-17:12 & Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases & Margaret Staton\\
17:14-17:19 & PLUTo: Phyloinformatic Literature Unlocking Tools & Ross Mounce\\
17:21-17:26 & A Publication Model that Aligns with the Key Open Source Software Principles & Michael L. Markie\\
17:27-17:30 & Announcements & \\
\hline
\textbf{17:30-18:30} & \textbf{Birds of a Feather (BOFs)} & \\
\hline
\textbf{19:00}-- & \textbf{\textit{Pay-your-own-way BOSC dinner}}, The Asgard Irish Pub and Restaurant & Limited seats, note \href{http://bit.ly/BOSC2014-dinner}{RSVP} only \\
\hline
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%\section*{Bioinformatics Open Source Conference (BOSC)}
\subsection*{BOSC Schedule - Day Two - Saturday, 12 July 2014}

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Time & Title & Author/Notes \\
\hline
8:55-9:00 & Announcements & \\
9:00-9:15 & Codefest 2014 Report & Brad Chapman\\
9:15-10:15 & \textbf{Keynote}: Biomedical Research as an Open Digital Enterprise & Philip Bourne\\
\hline
\textbf{10:15-10:45} & \textbf{Coffee Break} & \\
\hline
\textbf{10:45-12:30} & \textbf{\textit{Session: Software Interoperability}} & Chair: Raoul Bonnal\\
10:45-11:03 & Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization & Weijun Luo\\
11:03-11:21 & Use of Semantically Annotated Resources in the Mobyle2 Web Framework & Herv{\'e} M{\'e}nager\\
11:21-11:39 & Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms & Hilmar Lapp\\
11:39-11:57 & Integrating Taverna Player into Scratchpads & Robert Haines\\
11:57-12:15 & Small Tools for Bioinformatics & Pjotr Prins\\
\hline
\textbf{12:30-13:30} & \textbf{Lunch} & (Lunch and poster\\
\textbf{13:00-14:00} & \textbf{Poster Session and Birds of a Feather (BOFs)} & session overlap)\\
\hline
\textbf{14:00-15:30} & \textbf{\textit{Session: Open Science and Reproducible Research}} & Chair: Hilmar Lapp\\
14:00-14:18 & SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science & Carole Goble\\
14:18-14:36 & Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses & Brett Smith\\
14:36-14:54 & Enhancing the Galaxy Experience through Community Involvement & Daniel Blankenberg\\
14:54-15:12 & Supporting Dynamic Community Developed Biological Pipelines & Brad Chapman\\
15:12-15:30 & Open as a Strategy for Durability, Reproducibility and Scalability & Jonathan Rees\\
\hline
\textbf{15:30-16:00} & \textbf{Coffee Break} &\\
\hline
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16:00-17:00 & \textbf{Panel}: Reproducibility: Rewards and Challenges (Panelists: & Chair: \\
                    & Phil Bourne, C. Titus Brown, Varsha Khodiyar, Kaitlin Thaney) & Brad Chapman \\
17:00-17:10 & Presentation of Student Travel Awards and Concluding Remarks & \\
\hline
\textbf{17:10-18:00} & \textbf{Birds of a Feather (BOFs)} & \\
\hline
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\noindent
Please refer to \url{http://www.open-bio.org/wiki/BOSC_2014_Schedule} for the
latest schedule, including any changes since this document was prepared.

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\noindent
We thank \href{http://www.eaglegenomics.com}{Eagle Genomics} for
sponsoring the BOSC Student Travel Awards again this year, and welcome 
\href{http://www.gigasciencejournal.com/}{GigaScience} (an online
open-access open-data journal for `big-data' studies in the life and
biomedical sciences), and \href{https://curoverse.com/}{Curoverse}
(the team behind the open source platform \href{http://arvados.org/}{Arvados})
as new sponsors for BOSC 2014. We also thank
\href{https://developers.google.com/open-source/}{Google}
for their generous support for video-recording the talks at BOSC 2014.

~\\ \noindent % Force blank line; maybe I should change the template instead
\textbf{BOSC 2014 Organizing Committee:}
Nomi Harris and Peter Cock (Co-Chairs), Raoul Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp.

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