Monthly Archives: March 2005

Dev Log 2005-03-09

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New component: com_phpmyadmin261, embedded with BioMambo for databse management

  • Inspired by "phpmyadmin for mambo" http:/mamboforge.net/projects/mosphpmyadmin
  • The originall version is 2.5.7, we upgrade the thin wrapper for ver 2.6.1-p3
  • Administration backend only
  • Configured for http authentication, login with mysql account

Prepared three template (BioMambo_00x) for release

  • 001: based on vr_simpleportal
  • 002: based on ms_teamwork_452
  • 003: based on mambholic

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Apply extra controls to jobs or pipeline steps

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In webEngine, there is global setting at adminstration backend that
configures the default behavior of submitted job or pipeline steps.
These configurations include:

  • Whether to run jobs locally or let the batch system (LSF/SGE) to manage the
    jobs.
  • The default queue name for batch system.

Usually the default setttings are enough, but what if
certain job that requiremore subtle control on the way it runs. For
example, one "lintree" job must be submitted to a linux machine where
this program is available. Or, we expect a quick step in the pipeline
to be executed on the same host as previous step, so the time wont be
wasted in the batch system scheduling.

Web Engine supports very flexible control for both local job and LSF/SGE
jobs. The extra controls are applied when submitting the job or
configuring the pipeline steps.

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Bio.Mambo Project Overiew

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aa_world.gifBio.Mambo is a web portal solution based on the open source Mambo
project. We developed components that extend Mambo from a content
management system to a powerful portal for web-based bioinformatics
services and cluster management.

The Bio.Mambo project was
guided to work best with the knowledge from existing open source
projects. Based on Mambo’s web application framework, our development
time is significantly reduced by focusing on only the functions we
need.  Together with the components from other 3rd party
developers we are able to provide a complete portal solution for
bioinformatics cluster.

The components we developed for Bio.Mambo project include:

  • provides interfaces for more than 350 bioinformatics tools.
  • provides interface to design pipelines for various analysis.
  • manages pipeline jobs without persistent pipeline manager.
  • implements a DB-centric job management system.

  • Bio-Data Auto Updater
  • Parallel Local Data Distributor

  • Batch System Monitor (support LSF and SGE)

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Dev Log 2005-03-(05-08)

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"Web Engine"

  • Improved support for category, where sub-category is separated by :
  • Implementing jsCookMenu based menu navigation system
  • Implemented dtree based function map navigation system
  • Now navigation is perfect ;)
  • CSS logo for web eng�ne, read info directly from xml (xlst)
  • Add protocol information when gathering pipeline inputs.
  • Updated job conf page for tabbed control.

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Dev Log 2005-03-04

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  • Fixed a bug in GeSHI where user input & is not correct processed.
  • Fixed a bug in auto refresh javascript
  • Complete two pending tasks
  • Implemented subtle control over each job and step (local or lsf, extra controls for batch system: i.e. queue name, resource etc)
  • Implemented global parameters for pipeline. Global
    parameters will overwrite any local parameters for each step if the
    parameter name is the same

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Dev Log 2005-03-03

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"Web Engine" component

  • Fixed a serious bug in pipeline to run next steps, where jobs from other pipelines were incorrectly referred to.
  • Update protdist xml to support gamma value from either direct input or piped file
  • Between two steps, we allow only only relation.
  • Update neighbor XML file to remove bundled consense, pipeline forced
  • Fixed a bug in checkCompletion where pending jobs are not considered
  • Improved N-1 support where parameter from previous steps are also
    recorded. This could solve a previous problem where one job generates
    multiple pipeable outputs of the same pipetype and next piped step
    could not choose out of them.
  • Implemented support for pipe connections where there are multiple type output with multiple type input (clustalw–clustalw)
  • A GDD_loader as the single input entry for alan’s protocol
  • Enhanced auto-refresh page feature, job/pipeline image actionbar is disabled
  • Tabbed control for job/pipeline submission and step configuration

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Dev Log 2005-03-02

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"Web Engine" compoent

  • Implemented the new step sequence number system where step number
    is dynamically calculated by the relations among the steps. This is
    good for protocol design specially new steps have to be inserted
    between old steps.
  • Fixed a bug in protocol deletion where step relations are not removed
  • For each step in a protocol, there is clickable parameter list
  • For each job, there is a parameter list (cp_webengine_jobs schema changed)
  • Updated protocol job list with a new border for each job
  • Update protdist,neighbor,seqboot to use the same parameter name for "multiple data set" attribute
  • Improved display of long tool name, we display a shortened name instead
  • Update pipe support for multiple output files
  • if a piped file name results multiple files in file system, we run multiple jobs (non-pipeline)
  • for pipeline job, we restrict only one, if multiple files available, use first one
  • Alan’s
    gene duplication pipeline runs well, but the results is a little
    different from allison’s pipeline, not sure what’s wrong.. need to
    double check

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    Dev Log 2005-03-01

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    "Web Engine" component

    • Understand why codeml does not run well. The output from clustalw
      alignment can not be used by PAML directly even it is in PHYLIP format,
      it must be converted a little bit (read PAML doc for more)
    • Add one more step before codeml to convert the first
    • Improve prodist XML to support loading gamma from external file (Great hack with XML, feel it is so powerful and flexible)
    • Job command generation now supports get dynamic value form file’s content
    • Gene duplication protocol almost done. ;) By implementing this protocol, my web engine gets improved a lot.

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