Contents

How can I acknowledge HECBioSim in publications?
Why are there three different kinds of project?
Why was my application rejected based on a previous project containing unused resource allocation?
Why do projects that use certain codes not require an ARCHER technical assessment?
How long can a project last?
What should go into the 2 page scientific case?
What are my options if my application is rejected?
Can people overseas be listed as a project user?
Can PhD's/PDRA's apply as a PI?
Can purely industrial users apply?
What is the kAU and how many should I ask for?
When are the application deadlines?

 

How can I acknowledge HECBioSim in publications?

You should acknowledge both EPSRC and HECBioSim in any publications arising from your project, you should use the following test for this purpose:

This project made use of time on ARCHER granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/L000253/1)

 

Why are there three different kinds of project?

This is to make the application process as streamlined as possible for the applicant, there are three different kinds of project (pump-priming, standard and grand challenge). These projects typically utilise different scales of resource allocations and thus attract different levels of bureaucracy and approval.

Pump-priming - these projects are primarily for testing and proof of concept work, it is anticipated that these will be decided on an ongoing basis rather than going to the resource allocations panels. Applicants can request up to 1,200 kAUs of resource.

Standard - this is the most common type of project and falls within the 1,000 - 20,000 kAU range (with the 10,000+ kAU allocated only for exceptional projects). Because of the popularity and size of the allocations these applications will be decided by the resource allocation panel.

Grand Challenge - the grand challenge projects are typically 20,000-50,000 kAU and typically involve collaboration between many groups and many institutions and are aimed at tackling problems of high scientific significance/impact. These applications are unable to be assessed by the panel due to the scale of the application and the complexity and will be done via face to face meetings with the applicants.

 

Why was my application rejected based on a previous project containing unused resource allocation?

New project applications from applicants that have had previously successful applications and then subsequently went on to under use their allocation by 50% and upwards at the time the project closed, will be looked at. Project applications that fall into this category will likely be heavily penalised during the panel review.

 

Why do projects that use certain codes not require an ARCHER technical assessment?

The ARCHER technical assessment process is designed to ensure that codes are used effectively on this resource (scaling, job sizes and durations, etc.). In the case of the common MD codes, being used in “standard” ways, the consortium has sufficient existing knowledge of their performance to be able to by-pass this step. The current list of software that does not require you to get an ARCHER technical assessment is:

  • Amber
  • CHARMM
  • GROMACS
  • LAMMPS
  • NAMD

Should you feel that you know of software that should appear on that list then please get in touch and explain why you think it should be on the list. It may arise that the consortium could utilise your knowledge/expertise with such software such that we can broaden our support for software.

 

How long can a project last?

A project can last no longer than 6 months.

 

What should go into the 2 page scientific case?

The scientific case should include the following:

  • A basic scientific background to the study area and project goals.
  • A description of the proposed calculations and any preliminary/related work.
  • A brief assessment of potential impact of the project work.
  • References.

 

What are my options if my application is rejected?

Unfortunately due to the limited amount of ARCHER time at each HECBioSim panel and the high volume of applications for HECBioSim time on ARCHER, it is not always possible to accept every single application. If your application is rejected then your options include but are not limited to:

  • Submit another application to HECBioSim for the next decision panel (it will be subject to the same review process).
  • You can apply for various types of access to ARCHER directly from the ARCHER website here.

 

Can people overseas be listed as a project user?

No, users can be of any nationality but must be working/studying at a UK institution.

 

Can PhD's/PDRA's apply as a PI?

In short, no. The PI must be a permanent member of academic staff affiliated to a UK institution. Proposals sent by PhD students or post doctoral researchers will be rejected.

 

Can purely industrial users apply?

We are unable to offer time directly to industrial users, nor can we sell access or act as a commercial service provider. We do however welcome applications from collaborative projects between academic and industrial parties, often such projects will be ranked highly due to having an industrial collaborator. These collaborations are highly encouraged, do not require financial contribution from the industrial partner and can be quite broad in scope (methods development, test applications, studentships, code development, to try out ideas, etc).

 

What is the kAU and how many should I ask for?

The Allocation unit (kAU) can be thought of as a unit of computational work that is determined using the Linpack benchmarks, this unit is used as a measure of CPU time required in applications for HECBioSim applications for time on ARCHER. We have a calculator that can calculate the number of kAU's that would be required for a basic MD simulation using the codes we support, it is recommended that applicants make use of this, you can find it here. There is also a kAU calculator on the ARCHER website to assist one with working out how many kAUs a project will require if you are not using one of the codes that we support, the calculator can be found here.

 

When are the application deadlines?

The deadlines for which you can apply for time on ARCHER can be found here.