View source for Google Summer of Code 2015 Ideas

The details of each of our project ideas are listed below, including potential mentors. Interested mentors and students should subscribe to the OBF/GSoC [http://lists.open-bio.org/mailman/listinfo/gsoc mailing list] and announce their interest.

See the main OBF [[Google Summer of Code]] page for more information about the GSoC program and additional ways to get in touch with us.


==Cross-project ideas==

OBF is an umbrella organization which represents many different programming languages used in [http://en.wikipedia.org/wiki/Bioinformatics bioinformatics]. In addition to working with each of the "Bio*" projects (listed below), this year we are also accepting a category of "cross-project" ideas that cover multiple programming languages or projects. These collaborative ideas are broadly defined and can be thought of as "unfinished" &mdash; interested students should adapt the ideas to their own strengths and goals, and are responsible for the quality of the final proposed idea in their application.

'''Feel free to propose your own entirely new idea'''. You can also draw ideas from [http://gmod.org/wiki/GSoC#2014_Project_Ideas Genome Informatics (GMOD)] and the [http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2014 National Evolutionary Synthesis Center (NESCent)].

=== Provide Nextflow with a GUI based on NoFlo UI ===

; Rationale
: 
Nextflow is a data-driven toolkit for computational pipelines that simplify 
writing parallel and scalable pipelines in a portable manner. Its goal is to
make data analysis required by next generation sequence technologies and, in more 
general terms, bioinformatics applications easier for researchers. 
:
It follows the UNIX philosophy where many small tools can be composed together 
to create efficient computational solutions where individual parts can be easily
replaced. It has been designed to allow developers to fast prototype applications
reusing their existing tools and scripts. For this reason it has been developed 
primarily as a command line oriented tool. However, complex pipelines may benefit 
from having a visualisation layer that helps the developer design and represent 
the application workflow logic.
:
NoFlo-UI is the presentation layer for NoFlo, a flow-based programming (FBP)
environment that makes software creation more accessible and collaborative.
It provides an interactive interface which allows you to create a computational 
workflow by dragging, dropping and connecting the different task components. 
It basically allows you to "draw" an application in such a way that it resembles
a subway map. This "map" can then be more easily understood, shared and curated by 
other scientists, compared to managing endless files of source code.

; Approach
: 
The goal, therefore, of the this proposal is to implement a graphical front-end,
based on the NoFlo-UI project, for the Nextflow programming environment. This would 
provide the latter with a presentation layer that would allow researchers to "sketch" 
their computational pipelines instead of programming them, making it easier to share 
and handle complex task interactions in their application logic. 
: 
Ideally this integration will implement a two-way tool in such a way that 
changes, applied in the visual editor, are reflected in the Nextflow scripting 
language and vice-versa. 

; Languages and skills
: 
The student is required to have proven working ability with Javascript, HTML5, Polymer 
and Node.js for the front-end development and good level of knowledge of the Groovy/Java 
programming languages for Nextflow side. 
He/she may also benefit by having some theoretical and practical knowledge of programming 
language syntax and grammar parsers.

; Code
: 
Nextflow source code is available at the following repository (https://github.com/nextflow-io/nextflow/)
NoFlo-UI source code is available at this link (https://github.com/noflo/noflo-ui/)

; Mentors
: 
Paolo Di Tommaso

=== Nextflow low latency scheduling and in-memory data processing ===

; Rationale
: Nextflow is a data-driven toolkit for computational pipelines that simplify writing parallel and scalable pipelines in a portable manner across different execution platforms. Its goal is to make data analysis required by next generation sequence technologies and, in more general terms, bioinformatics applications  easier for researchers.

: Nextflow does not implement a task scheduling strategy on its own but delegates it to the underlying processing infrastructure, which in most cases is a grid engine like technology (SGE, PBS, SLURM, etc). However, these platforms were designed for job processing in a batch scheduling fashion, i.e. a few long duration jobs scheduled sequentially to the computer-cluster facility. This model suffers from very high latencies which make it unfit for highly parallel and short-lived jobs that are more and more common in bioinformatics  data analysis.

: The goal of this proposal is to integrate the Sparrow scheduler and Tachyon in-memory file system with Nextflow to overcome the limitations of batch-like schedulers generally available in most common cluster computation facilities.

: The first is a high throughput, low latency distributed cluster scheduler, while the second is a memory centric distributed file system. Both of them are open source research projects developed at UC Berkeley.

: The integration of these technologies would allow Nextflow to manage large distributed workloads in a more efficient and timely manner and to decrease the task granularity in Nextflow pipelines. Thus gaining an higher parallelism degree and better applications performance.

; Approach
: Nextflow implements an extensible mechanism that allows it to support several computing platforms and file systems in a portable manner. 
: The approach suggested consists in implementing a new Nextflow executor which integrates the Sparrow scheduler and its features. 
: The support for Tachyon file system can be added to Nextflow by writing an adapter layer that follows the Java JSR-203 specification.

; Languages and skills
: Student is required to have proven working ability with the Java and/or Groovy programming languages and a good level of theoretical and practical knowledge in parallel and concurrent programming. 

; Code
: Nextflow source code repository (https://github.com/nextflow-io/nextflow)
: Sparrow cluster source code (https://github.com/radlab/sparrow)
: Tachyon file system source code (https://github.com/amplab/tachyon) 

; Mentors
: Paolo Di Tommaso

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
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; Code
: TEXT HERE TEXT HERE

; Mentors
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==[http://bioperl.org/wiki/Google_Summer_of_Code BioPerl]==

[[Image:BioPerl_logo_tiny.jpg|right|link=bp:Google Summer of Code]]

* [[bp:Mailing_lists|Mailing lists]]
* IRC: <code>#bioperl</code> on [http://freenode.net Freenode]
* [[bp:Becoming_a_developer|Information for new developers]]
* Source code browser for [https://github.com/bioperl/bioperl-live bioperl-live] (the main BioPerl code base), and [https://github.com/bioperl all BioPerl sub-projects]
* [[bp:Project_priority_list|Priority list]] of things that need work, as another source for student-conceived project ideas 

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
: TEXT HERE TEXT HERE 

; Code
: TEXT HERE TEXT HERE

; Mentors
: TEXT HERE TEXT HERE 


==[http://biojava.org/wiki/Google_Summer_of_Code BioJava] and JSBML==

[[Image:Biojava_logo_tiny.jpg|right|link=http://biojava.org/wiki/Google_Summer_of_Code]]

* [http://lists.open-bio.org/mailman/listinfo/biojava-dev BioJava developer mailing list]
* [https://groups.google.com/forum/#!forum/jsbml-development JSBML developer mailing list]
* [http://biojava.org/wiki/BioJava:Modules BioJava modules] as another source for student-conceived project ideas
* Source code for [http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk biojava-live] (the main BioJava code base) and [http://code.open-bio.org/svnweb/index.cgi/biojava/ all BioJava sub-projects]

For GSoC 2014, BioJava is partnering with the Systems Biology Markup Language (SMBL) team to bring enhancements to JSBML, the standard Java implementation of SBML, and bring SBML features to other Java-based systems biology software. See [http://sbml.org/GSoC2014 the SMBL website] for more ideas from the SBML team.

Students working on these projects will interact with both the BioJava and JSBML communities, which overlap. Most development will happen on the JSBML codebase, although BioJava is used as a supporting library for some components.

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
: TEXT HERE TEXT HERE 

; Code
: TEXT HERE TEXT HERE

; Mentors
: TEXT HERE TEXT HERE 



==[[biopython:Google Summer of Code |BioPython]]==

[[Image:Biopython_logo_tiny.png|right|link=biopython:Google Summer of Code]]

* [[biopython:Mailing lists|Mailing lists]]
* [[biopython:Contributing|Information for contributors]]
* [[biopython:SourceCode| Source Code]]

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
: TEXT HERE TEXT HERE 

; Code
: TEXT HERE TEXT HERE

; Mentors
: TEXT HERE TEXT HERE 



==[http://bioruby.open-bio.org/wiki/Google_Summer_of_Code BioRuby]==

[[Image:BioRuby_logo_tiny.png|right|link=http://bioruby.org]]

* [http://lists.open-bio.org/mailman/listinfo/bioruby Developers mailing list]
* [http://github.com/bioruby/bioruby/tree/master Source code]
* IRC: <code>#bioruby</code> on [http://freenode.net Freenode]

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
: TEXT HERE TEXT HERE 

; Code
: TEXT HERE TEXT HERE

; Mentors
: TEXT HERE TEXT HERE 



==[http://biohaskell.org/Google_Summer_of_Code BioHaskell]==

:* [http://biohaskell.org/ Project website]
:* [http://hackage.haskell.org/packages/#cat:Bioinformatics Bioinformatics section on HackageDB]
:* [http://biohaskell.org/Google_Summer_of_Code GSoC page]

Biohaskell has its own gsoc page. We currently have 2 (+1) open problems listed there. In addition, we accept peoples' own ideas and have a number of open problems not listed. The latter fall somewhere between bachelors thesis and PhD work and are harder to nicely package up.

=== Fast k-mer indexing ===

Fast k-mer indexing requires a data structure mapping a short string of k characters to a value. While trivial to do with almost all key-value maps, we also require a very memory-efficient storage system. Knowledge of suffix structures is a definite plus.

; Mentors
: Ketil Malde?

=== Low-level bit and stream-fusion optimizations ===

In Haskell, we typically don't talk that much about low-level implementation details. For some algorithms, low-level details (especially bitwise operations and SIMD instructions) become important. I have a library dealing with bitsets but it is not yet fully efficient. Getting SIMD instructions to play nice with /generic/ DP recursion schemes is probably really hard.

; Mentors
: Christian Hoener zu Siederdissen



==[http://biocaml.org Biocaml]==
:* [https://groups.google.com/d/forum/biocaml Mailing List]

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
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; Languages and skill
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; Code
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; Mentors
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== Candidate a new project for OBF ==
Please if you want to be part of OBF but you porject is not yet listed above, contact us and let us know about your project and your proposal.

=== TITLE ===

; Rationale
: TEXT HERE TEXT HERE 

; Approach
: TEXT HERE TEXT HERE 

; Languages and skill
: TEXT HERE TEXT HERE 

; Code
: TEXT HERE TEXT HERE

; Mentors
: TEXT HERE TEXT HERE 


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