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Computational Biology

▶ How to getting started quickly?

Getting started on LSU systems requires several steps that may vary depending on how experienced you are with HPC systems. The items listed here are not meant to be exhaustive - treat as robust starting points.

Everyone

Every LONI and HPC system user requires a user account. Some systems also require an allocation account to charge production runs against.

  1. Visit the applications index to see what software is currently installed. Listings by name and by field (i.e. Computational Biology) are provided. Assistance with installing other software is available.
  2. Request a LSU and/or LONI user account. Individuals on the LSU campus have access to both sets of resources.
  3. Be aware that assistance in many forms is always available.

Production efforts on LONI and some LSU resources (i.e. SuperMike-II) require an allocation of system time in units of core-hours (i.e. SU) against which work is charged. This is a no-cost service, but a proposal of one form or another is required. The holder of an allocation then adds users who may charge against it. Note that only faculty and research staff may request allocations (see allocation policy pages for details).

To request or join an allocation, you must have the appropriate system user account and then visit:

  1. LSU allocation applications (e.g. SuperMike-II).
  2. LONI allocation applications (e.g. QueenBee, Eric, etc.).

Beginner

See the Training link for the various forms of training that are available, such as: Moodle courses, weekly tutorials (live and recorded past sessions), and workshops.

  1. Learn how to connect to an HPC system (SSH, PuTTY, WinSCP).
  2. Learn basic Linux commands.
  3. Learn how to edit files (vi/vim editor).
  4. Learn about the user shell environment (bash shell).
  5. Learn how to submit jobs (PBS)

Advanced

  1. Learn how to manage data files.
  2. Learn how to control your applications of choice.
  3. Learn how to write shell scripts (i.e. job scripts).
  4. Learn how to install custom software.
  5. Learn to program in one or more languages.

Expert

  1. Learn how to debug software (ddt, totalview).
  2. Learn how to use parallel programming techniques.
  3. Learn how to profile and optimize code (tau).
  4. Learn how to manage source code (svn).
  5. Learn how to automate the build process (make).

▶ What applications are installed?

The following applications are installed and maintained at the mostcurrent release level (currently on Super Mike 2 only). Some of the more heavily used applications areinstalled with their own Softenv keys, but most are grouped under keysby functionality. This pages provides an alphabetical listing of allthe apps with links to their respective home pages - the best place tofind documentation. Those who need a specific version are welcome toinstall copies in their own file space.

▶ Genome alignment tools?

The available genome alignment tools include:

▶ RNA sequence alignment tools?

The available RNA sequence alignment tools include:

▶ Genome assembly tools?

The available genome assembly tools include:

▶ Transcriptome assembly tools?

The available transcriptome assembly tools include:

▶ Sequence comparison/alignment tools?

The available sequence comparison/alignment tools include:

▶ Recombination evaluation tools?

The available recombination evaluation tools include:

▶ Pipelines?

The available computational biology pipeline toolsets include:

▶ Phylogenics tools?

The available phylogenetics tools include:

▶ GPU-enabled tools?

The available GPU-enabled computational biology tools include:

▶ Miscellaneous tools?

Some other miscellaneous computational biology tools include:


Users may direct questions to sys-help@loni.org.