Changes between Version 39 and Version 40 of WikiStart

2009/02/06 21:32:50 (15 years ago)



  • WikiStart

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    7 == Hackathon == 
    9 The hackathon (hacking + marathon) basically is a camp where invited participants discuss about 
    10 current issues and implement software to solve the problems on site collaboratively. 
    11 This kind of meeting is very effective for the intensive development of projects, because 
    12 face-to-face meeting of developers who are usually spread around the world, accelerates 
    13 communication and collaboration to exchange their ideas. 
    15 !BioHackathon is a hackathon to implement bioinformatics software towards domain specific goals. 
    16 This year, we will focus on end user applications to make our previous standardization efforts in 
    17 [ BioHackathon 2008] 
    18 to be fully utilized by the primary users of our infrastructure. 
    19 For this purpose, we will also involve semi-wet biologists working in an area where 
    20 high throughput genome annotation is required. 
    21 By knowing their demands, we will be able to find what kinds of resources are missing and 
    22 to prioritize our action items. 
    24 == Purpose == 
    26 Main purpose of the meeting is to continue global efforts to standardize 
    27 biological database resources and to improve usability and interoperability 
    28 of bioinformatics services, which were proposed in the previous meeting. 
    30 The agenda of the previous meeting, !BioHackathon 2008, is available at 
    34 Additionally, we will collaborate with 
    36  * Organizations which have similar mission with us (e.g. ELIXIR) for the complementary efforts. 
    37  * Developers of integrated platforms like !BioMart, GMOD, Galaxy etc. 
    39 to make our previous efforts to be utilized by the scientific researchers effectively. 
    41 == Topics == 
    43 Technology: Infrastructure and standardization 
    45  * Integration of the integrated databases - Unified API for distributed services 
    46  * Agreement on common exchange data formats, ontologies and semantics 
    47  * Provide stable and interoperable services with SOAP and REST 
    48  * Manifesto and guidelines for the next generation web services 
    50 Application: Mash-up and user friendly interface 
    52  * Improve end-user applications like Galaxy to utilize integrated databases and services 
    53  * What kinds of resources are currently missing for science? 
    54   * e.g. Genome-scale analysis: pipelines and visualization 
    56 Promotion: Outreach to the wet biologist 
    58  * Hands-on seminar 
    59  * Documentation 
    617== Objectives == 
    63  * Solve several use cases and summarize in tutorials during the hands-on seminar 
     9In the [ BioHackathon 2008], we have focused on the standardization of bioinformatics web services and the exchange data formats to create bioinformatics workflows. To make these global efforts to be fully utilized by the biologists, we need to integrate these services into the various end-user applications. 
    65  * Discuss about the guidelines (manifesto) towards standardization of 
    66    data types and protocols for the integration of databases and services. 
     11For this purpose, we will organize the second BioHackathon gathering software developers of mash-up services and web service providers. Additionally, to solve the real world use cases, we will also involve semi-wet biologists to apply their data for testing these services and applications in combination. 
    68  * Improve Open Bio* libraries and other tools to apply real world issues. 
     13Our goal is to develop stable and usable platforms for emerging demands, such as 
    70  * Publication of a meeting report. 
     15 * Workflow for the massive sequence annotation (Galaxy, BioMart, Taverna, MOWserve etc.) 
     16 * Automatics genome sequence assemble and mapping (GMOD/GBrowse, UTGB etc.) 
     17 * Visualization of the large scale data sets (Cytoscape, Processing etc.) 
     18 * Interoperable web services and database resources (BioMOBY, TogoWS, TogoDB etc.) 
     20and test these infrastructures with several biological use cases. 
     22For example, the Marine Genomics Unit in OIST equipped with Roche 454 sequencers and they are hoping to start environmental genomics of the coral reef in Okinawa. We have been working  
     23on the integration of our database resources into the Galaxy, and would like to offer them to use the services provided by the DBCLS. Additionally, we will start to select some suitable use cases to deal with, based on the discussion in the mailing list. 
     25BioHackathon 2009 is sponsored by the Database Center for Life Science (DBCLS) and Okinawa Institute of Science and Technology (OIST), and will be held in Tokyo and Okinawa, Japan. 
     27 * BioHackathon 2009 
     28 * BioHackathon 2008 
     29 * DBCLS 
     30 * OIST 
     32The DBCLS is being accepted as a national center for the sustainable life science databases in Japan. The OIST is the graduate university of science and technology and aiming to create a leading intellectual hub in the Asian-Pacific region. 
     34== Expected outcomes == 
     36* Improve end-user applications like Galaxy or Taverna by testing with the use cases. 
     37* Document how to solve the biological problems using these softwares and resources based on the hands-on seminar. 
     38* Issue a manifesto and guidelines for creating interoperable web services with SOAP and/or REST. 
     39* Publication of the meeting report. 
     41=== About the Hackathon === 
     43The hackathon (hacking + marathon) basically is a camp where invited participants discuss about current issues and implement software to solve the problems on site collaboratively. This kind of meeting is very effective for the intensive development of projects, because face-to-face meeting of developers, who are usually spread around the world, accelerates communication and collaboration to exchange their ideas. 
    7245== Mailing list ==