From Bioinformatics.Org Wiki

[return to BIRCH on HPC systems]

---

Contents 1 Meeting to discuss BIRCH on Grex and other Alliance Can. systems 1.1 Introductions 1.2 Quick Intro to BIRCH and BioLegato 1.2.1 Users' Perspective 1.2.1.1 BIRCH 1.2.1.2 BioLegato - Ease of Use 1.2.2 Sysadmins' Perspective 1.2.2.1 BIRCH 1.2.2.2 BioLegato 1.3 Implemention of BIRCH on Grex, other DCA systems 1.3.1 How was the BIRCH app implemented? 1.3.2 Issues to solve: 1.3.2.1 Java needs to be in the default $PATH 1.3.2.2 Version management 1.3.2.3 Who will have write privileges for $BIRCH/local? 1.3.2.4 Can $BIRCH/public_html be made publicly available? 1.3.2.5 Just about any of the bioinformatics software currently on DAC could be integrated into BIRCH using links from $BIRCH/local/script, $BIRCH/local/bin-linux-x86_64 etc. 1.4 Are there other disciplines that could benefit from BioLegato? 1.5 Action Items

Meeting to discuss BIRCH on Grex and other Alliance Can. systems

Date: March 18, 2026
Location: EITC E2-588
Attendees:
Dr. Brian Fristensky, Plant Science
Grigory Shamov
Stefano Ansaloni

Introductions

Names, Affiliations, What do you do?

Quick Intro to BIRCH and BioLegato

Users' Perspective

BIRCH

• One package has hundreds of commonly used bioinformatics programs
• Lots of tutorials and videos
• Use BIRCH on laptop or on HPC system
• BioLegato GUI ties together hundreds of applications seamlessly

BioLegato - Ease of Use

• GUI is less intimidating than command line
• Menus minimize mistakes, protects user from themselves
• enforces good practices eg. sanity checking before running a program
• Leverages Object-oriented concepts that incorporate biological a world-view
  • Each Biolegato application is a different class

Sysadmins' Perspective

BIRCH

• Almost all aspects of system administration are run through BioLegato GUI
  • Managing local BLAST databases is done using blastdbkit.
• $BIRCH/local - seamlessly integrate locally-installed programs and documentation into BIRCH
  • Example: Local customization of BIRCH web pages
  • Local additions are re-integrated with each update

BioLegato

• Adding new programs to BioLegato is almost as easy as filling in a form
• Any new BioLegato menu added to $BIRCH/dat is automatically integrated into BioLegato the next time it is launched.
• BioLegato is now a standalone project on GitHub

Implemention of BIRCH on Grex, other DCA systems

How was the BIRCH app implemented?

Issues to solve:

Java needs to be in the default $PATH

Version management

The current design of BIRCH requires persistence of $BIRCH/local when an update is done. Install scripts will make some changes to $BIRCH/local to accommodate new features and delete obsolete ones

Who will have write privileges for $BIRCH/local?

Can $BIRCH/public_html be made publicly available?

eg. as a symbolic link?

Just about any of the bioinformatics software currently on DAC could be integrated into BIRCH using links from $BIRCH/local/script, $BIRCH/local/bin-linux-x86_64 etc.

Are there other disciplines that could benefit from BioLegato?

Fields in which there are

• large and growing body of command line tools used
• extensive learning curve for each tool
• many different file formats
• frequent pipelineing of output from one tool as input to the next tool

eg. chemistry, geology, astronomy, engineering, meteorology?

Action Items