BMDExpress2 2.30.0502

BMDExpress 2 is a desktop application for Windows, Mac or Linux (See IMPORTANT warning) that enables analysis of dose-response data produced in differential gene expression experiments. It provides stepwise workflows that combine benchmark dose (BMD) calculations with functional classification analysis based on Gene Ontology (GO), Signaling Pathways (Reactome), or custom categories provided by the user. The end results are estimates of doses at which cellular processes are altered, based on an increase or decrease in response in expression levels compared to untreated controls. All of the dose-response curve fit models utilized by BMDExpress 2 are those contained within USEPA BMDS software.

Accessing BMDExpress2 2.30.0502

To load the module for BMDExpress2 2.30.0502 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load BMDExpress2/2.30.0502

BEAR Apps Version

2020b

Architectures

EL8-cascadelake — EL8-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the BMDExpress2 website.

Dependencies

This version of BMDExpress2 has a direct dependency on: Java/11

Last modified on 27th August 2021