NEWS: Light-weight version now running until April 2027.
CompBioMed offers a free light-weight scaling support to improve the performance of your computational biomedicine solutions on high performance computers
Whether you work in academia, in a research hospital, or in a company, there is a good chance that you are starting to make intensive use of the computational biomedicine applications you have developed. As these evolve, you may be discovering performance issues.
Are you struggling because your code cannot run in an acceptable time? Perhaps you are trying to simulate over 1000 virtual patients? Or do you simply need to do some large-scale sensitivity analysis to get your solution certified by the regulatory authority?
Whatever is the reason, we can help. Thanks to a small group of experts in High Performance Computational Biomedicine, we now offer free, light-weight advice line to individuals and/or organisations in specific questions about HPC, certain biomedical applications or even their initial steps towards parallelising existing computational biomedicine applications, or improving the scalability of those applications already parallelised, and then deploying them on high performance computing resources. We can answer your questions directly or point you towards the relevant experts.
This Service is open to all: not only to both CompBioMed Core and Associate Partners, but it is also open to individuals and organisations new to CompBioMed.
Contact us via our email list compbiomed-support@ucl.ac.uk.
We no longer offer to review, port, profile and/or adapt source code, and any requests for large amounts of effort to review/port/profile/adapt source code will be forwarded to Innov4Scale, and/or the relevant HPC centre/expert; however, we do offer light-weight advice on HPC in general
- General
- What is HPC
- Exascale
- Training
- HPC Services
- Porting serial applications to HPC
- Scaling parallel applications
- Co-design
- Containerisation
- Data Services
- Data Management
- Data publishing
- Data formats
- Metadata Schemas
- Data movement
- Data Analysis
and on the following applications
- Cardiovascular
- Alya, Chaste, HemeLB, HemoCell, openBF, Palabos, PolNet, Living Heart Human Model
- Molecular
- BAC, Antibiotic Resistance, ACEME, HTMD, TorchMD, AdaptiveBandit, PlayMolecule, DNAnexus, VisualGec, HTBAC, Virtual Assay, SIMULIA LHHM, MonoAlg3D
- NMS
- CT2S, ARF10, Insigneo Bone Tissue Suit, Vertebroplasty Simulator, XCT2FE, BoneStrength
- Others
- MuscleHPC, pFIRE, InSilicoMRI, BBCT
To access this light-weight Service, simply email compbiomed-support@ucl.ac.uk
- We no longer offer the following additional access routes
- Application Form: To enter into an official collaborative relationship with CompBioMed, then please complete this application form (link) and send it using this link.
- Web form: The Application Form (above) is highly detailed, so we also provide a simpler more light-weight web form here.
- In Silico World: The CompBioMed team are experts in both High Performance Computing and biomedical applications, can also answer your questions via the #scalability public channel provided within the In Silico World Community of Practice hosted on Slack. To enter the community, contact "info at insilico.world" referring to CompBioMed or visit the page here.
Programmers' resources
A useful technical overview (Crib Sheet) for programmers, with tips to improve the scalability of their applications with a view to porting to the latest Supercomputers: Rough Guide to Preparing Software for Exascale.
Code and Data Security
In the field of biomedicine, many applications deal with sensitive data, and you can be assured that we will take great care when adapting your applications and managing the associated data. Our Data Policies cover data privacy, data security, and research data management, and can be found here. In particular, with the data security policy, we describe how we ensure the security of data or source codes that you share with us.
Terms and Conditions
The full Scalability Service used to follow CompBioMed's Terms and Conditions (link); however, this full Service closed 1st April 2024.
This new light-weight continuation, running until 1st April 2027, is now a "best-effort" service, where questions will be answered either directly, by our own team of volunteer CompBioMed experts in HPC Biomedicine, or by pointing you towards the relevant expert.