BioHPC Guides

BioHPC tries to provide a wide range of services, accessible through easy web-based cloud services as well as more traditional command line access. The guides section of the portal covers topics of interest to a variety of users to complement our training calendar. Though we try to deliver a comprehensive set of training sessions there isn't time for us to cover everything - so we'll put additional material here. Guides will be added as time allows, and in response to common user queries or common themes we notice. Some pages will be tutorials, while others will be quick-reference sets of FAQs.

If you think we should add a guide about a particular topic please let us know via


Cloud Services

Our Cloud Services, including web job submission, the webGUI, nucleus web terminal, and lamella/cloud storage systems provide easy access to BioHPC compute and storage facilities. These services are covered heavily in our introductory and basic training sessions. Users are encouraged to attend these sessions to familiarize themselves with the cloud services.


Accessing the Nucleus Compute Cluster (SSH / File Transfer / remoteGUI sessions)

Note - The Nucleus cluster can be accessed via the web terminal, and files transferred using the lamella cloud storage system. These guides are for advanced users wishing to use SSH and file transfer clients from a laptop or desktop computer.

  • Guide - Connecting to Nucleus from Mac OSX 
  • Guide - Connecting to Nucleus from Windows
  • Guide - Transferring Files to/from BioHPC using FTP
  • Guide - Starting and Connecting to remoteGUI cluster GUI sessions



Matlab is the most heavily used software on the nucleus cluster.

  • FAQs - Matlab Frequently Asked Questions



The SBGrid consortium maintains a collection of structural biology software, and distributes this software collection to members. The BioHPC cluster and clients have access to SBGrid, which can also be mounted to other machines on campus.