DNAMA

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== General Information ==
== General Information ==
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* Application's name: DNA Multicore Analysis
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* Application's name: ''...''
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* Virtual Research Community: Life Sciences
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* Application's acronym: ''...''
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* Scientific contact: ''Danilo Mrdak, danilomrdak@gmail.com''
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* Virtual Research Community: ''...''
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* Technical contact: ''Luka Filipovic, lukaf@ac.me''
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* Scientific contact: ''...''
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* Developers: ''Center of Informatin System - University of Montenegro, School of Computer & Communication Sciences Laboratory for Computational Biology and Bioinformatics, ''
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* Technical contact: ''...''
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* Web site: -
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* Developers: ''...''
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* Web site: ...
== Short Description ==
== Short Description ==
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Using of Network Cluster Web with potential of super-computer performances for DNA sequences analyzing will give us unlimited potential for DNA research. This will give us unlimited potential in term of analyzed sequence number and time consumption for analysis to be carried out. As many of DNA comparing and analyzing software use Monte Carlo and Markov chain algorithms that are time consuming regarding to sequence numbers, super-computer resource will faster our job and make the robust and overall analysis possible.Using of all published sequences for one group (e.g. for all salmonid species: salmons, trout, grayling, river huchon) from the same DNA region (mitochondrial D-loop DNA, Cytochrom b gene…) will give us more detailed insight in their relationships and phylogeny relationships.
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== Problems Solved ==
== Problems Solved ==
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The working resource that is possible to use trough network computer clustering will allow us to put in analysis as much samples as we wish and that those analysis will be finished in one to few hours. Moreover, we will tray to modified the algorithms in order to have multi-loci analysis to get a consensus three that will suggest the most possible pathways of phylogeny with much higher level of confidence
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== Scientific and Social Impact ==
== Scientific and Social Impact ==
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''Tobefilledin''
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...
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== Collaborations and Beneficiaries ==
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...
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''Tobefilledin''
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== Collaborations ==
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* ...
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* ...
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== Beneficiaries ==
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* ...
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* ...
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== Number of users ==
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...
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== Development Plan ==
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* Concept: ''...''
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* Start of alpha stage: ''...''
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* Start of beta stage: ''...''
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* Start of testing stage: ''...''
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* Start of deployment stage: ''...''
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* Start of production stage: ''...''
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== Resource Requirements ==
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* Number of cores required for a single run: ''...''
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* Minimum RAM/core required: ''...''
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* Storage space during a single run: ''...''
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* Long-term data storage: ''...''
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* Total core hours required: ''...''
== Technical Features and HP-SEE Implementation ==
== Technical Features and HP-SEE Implementation ==
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* Primary programming language: ''C''
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* Primary programming language: ''...''
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* Parallel programming paradigm: ''MPI, OpenMPI''
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* Parallel programming paradigm: ''...''
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* Main parallel code: ''MPI, OpenMPI''
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* Main parallel code: ''...''
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* Pre/post processing code: ''C''
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* Pre/post processing code: ''...''
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* Application tools and libraries: ''RAxML''
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* Application tools and libraries: ''...''
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* Number of cores required: ''up to 1024''
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* Minimum RAM/core required: ''1 GB''
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* Storage space during a single run: ''256 MB''
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* Long-term data storage: ''1 GB''
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== Usage Example ==
== Usage Example ==
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''Tobefilledin, text and (maybe) images.''
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...
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== Infrastructure Usage ==
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* Home system: ''...''
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** Applied for access on: ''...''
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** Access granted on: ''...''
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** Achieved scalability: ''... cores''
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* Accessed production systems:
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# ''...''
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#* Applied for access on: ''...''
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#* Access granted on: ''...''
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#* Achieved scalability: ''... cores''
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# ''...''
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#* Applied for access on: ''...''
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#* Access granted on: ''...''
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#* Achieved scalability: ''... cores''
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* Porting activities: ''...''
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* Scalability studies: ''...''
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== Running on Several HP-SEE Centres ==
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* Benchmarking activities and results: ''...''
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* Other issues: ''...''
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== Achieved Results ==
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...
== Publications ==
== Publications ==
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* ...
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* ...
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== Foreseen Activities ==
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* ...
* ...
* ...
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Revision as of 11:53, 13 February 2012

Contents

General Information

  • Application's name: ...
  • Application's acronym: ...
  • Virtual Research Community: ...
  • Scientific contact: ...
  • Technical contact: ...
  • Developers: ...
  • Web site: ...

Short Description

...

...

Problems Solved

...

Scientific and Social Impact

...

...

Collaborations

  • ...
  • ...

Beneficiaries

  • ...
  • ...

Number of users

...

Development Plan

  • Concept: ...
  • Start of alpha stage: ...
  • Start of beta stage: ...
  • Start of testing stage: ...
  • Start of deployment stage: ...
  • Start of production stage: ...

Resource Requirements

  • Number of cores required for a single run: ...
  • Minimum RAM/core required: ...
  • Storage space during a single run: ...
  • Long-term data storage: ...
  • Total core hours required: ...

Technical Features and HP-SEE Implementation

  • Primary programming language: ...
  • Parallel programming paradigm: ...
  • Main parallel code: ...
  • Pre/post processing code: ...
  • Application tools and libraries: ...

Usage Example

...

Infrastructure Usage

  • Home system: ...
    • Applied for access on: ...
    • Access granted on: ...
    • Achieved scalability: ... cores
  • Accessed production systems:
  1. ...
    • Applied for access on: ...
    • Access granted on: ...
    • Achieved scalability: ... cores
  2. ...
    • Applied for access on: ...
    • Access granted on: ...
    • Achieved scalability: ... cores
  • Porting activities: ...
  • Scalability studies: ...

Running on Several HP-SEE Centres

  • Benchmarking activities and results: ...
  • Other issues: ...

Achieved Results

...

Publications

  • ...
  • ...

Foreseen Activities

  • ...
  • ...
Retrieved from "http://hpseewiki.ipb.ac.rs/index.php/DNAMA"
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