Faq

From Chasm Software Wiki

Frequently Asked Questions

• Are CHASM and SNVBox open source?
  • Yes! Both softwares are open source and are subjected to the terms of the JHU Software License. It is free for academic use but needs to be licensed for commercial use from Johns Hopkins Technology Transfer.
• Why do CHASM scores for the same mutation change after updating the SNV-Box database?
  • CHASM is a data driven method. With each update of our database, feature values retrieved for each mutation may change slightly because of changes in the set of catalogued Refseq, CCDS, Ensembl and Swissprot proteins, changes in the NR database used to construct multiple sequence alignments, or changes in other features. Any significant feature changes between SNV-Box releases that may impact classification results will be announced on the website. It is advised that classifiers should be retrained periodically to take into account changes in the SNV-Box database. The performance of the algorithm is expected to improve as the amount of data available increases.
• Why do different classifiers trained using the same context table score the same mutations differently?
  • The set of known driver mutations is updated periodically, and the passenger generation process is a random process, therefore the training set used to train each classifier is different at each run. However, the scores assigned to the same mutation by different classifiers built using the same context table should not differ significantly.
• Can I contribute to CHASM's development?
  • We haven't really worked out the details for that kind of collaboration yet, but please contact us if you are interested in contributed additional algorithms or supplying additional features which we can add into SNV-Box.
• How do I report bugs?
  • Please open a Bugzilla account and file a bug under the appropriate product and component. The bugs are divided under the product names CHASM, SNVBox and Classifier Pack.
• I cannot retrieve proteins by UniProtKB Accession Identifiers, is there something wrong?
  • We currently only support Refseq, CCDS and Ensembl mRNA transcript and protein Accession Identifiers. We do not support UniProtKB identifers.
• The thing attached to the Box in the SNVBox logo, is it really a nose?
  • Yes it is!
• How can I build my own passenger mutation rate table?
  • There are several ways to do this, but a simple protocol is outlined here.
• Is there any script I can run to generate a passenger mutation rate table for me?
  • Currently no but it is under-development.
• Help! I'm getting an error message regarding a system variable called $CHASMDIR
  • (See below)
• Help! I'm getting ELF error or other linkage issues when I try to run the binaries

There are two environmental variables that need to be set for the software to run.
The CHASM binaries learn the location of the CHASM installation through a system
variable called $CHASMDIR. The Linux system learn where to find the shared object
library files needed to execute the CHASM binaries from $LD_LIBRARY_PATH.

You need to run
> export CHASMDIR=[CHASM Installation Directory]
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CHASMDIR
in your session first before running any of the CHASM binaries.

You may want to add those two lines to your ~/.bashrc file.