Towards a Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) and bridging the gaps between structure determination methods

Lead Research Organisation: STFC - Laboratories
Department Name: Scientific Computing Department

Abstract

Understanding how cells work is vital to combating disease. While experimental techniques such as macromolecular crystallography and nuclear magnetic resonance spectroscopy have for many years given detailed information on important molecules in the cell, attention is now moving to how these molecules interact with each other and how they are affected by their location in the cell. Electron cryo-Microscopy (cryo-EM) provides very useful information here, and bridges the gap between individual molecules and the whole cell. In the most favourable cases, detailed images of assemblies of molecules can be obtained, while at lower resolutions electron tomograms can show slices through cells or tissues. Advances in instrumentation and data processing have led to a significant increase in the application of cryo-EM in recent years, such that it is now one of the most important experimental techniques available in structural and cellular biology.

To exploit fully cryo-EM requires good software for processing the primary experimental data and for interpretating it in terms of molecular or cellular structure. However, software provision is patchy and fragmented, and individual labs face a steep learning curve when trying to create a suitable software environment for their projects. The macromolecular crystallography community faced such a challenge more than 30 years ago, and the Collaborative Computational Project No. 4 (CCP4) was created to address this challenge. In the years following, CCP4 has grown to be a major international project, and has underpinned many of the advances in our understanding of cells at the molecular level. In the last 10 years, the sister project CCPN has performed a similar role for the nuclear magnetic resonance spectroscopy community. The field of cryo-EM needs a similar initiative, and this proposal is a first step in that direction.

There are at least 25 groups in the UK active in the field of cryo-EM. We are proposing a Partnership open to all UK groups with the aim of establishing a Collaborative Computational Project (CCP-EM). The CCP-EM will coordinate efforts within the UK community. It will support users through dissemination of information on available software, helpdesk support, and directed training. It will support developers through technical help and by helping to distribute their software to the community. Gaps in software provision will be identified, and where feasible new software written.

The Partnership will lead to a better use of software within UK groups. It will relieve some of the burden connected with understanding and installing a wide range of incompatible software. The support of a dedicated group of scientists will greatly speed up the process of establishing new groups or helping established microscopists move into new areas (such as tomography). However, the most important output is the development of a community spirit, that encourages individual scientists to pool their efforts. The creation of scientific communities in the UK leads to the best use of public money, and maximises the return on the UK's investment in microscopy facilities.

Technical Summary

The Partnership will address three broad areas: It will provide a forum for planning a Collaborative Computational Project (CCP) in cryoEM, and for developing a roadmap for future software developments. It will support the users of software for cryoEM through dissemination of information on available software, directed training and improvements to the useability of software. Finally, it will provide support for software developers, including porting, optimisation and distribution of software.
These aims will be achieved through two computational scientists based at the Research Complex at Harwell, directed by 7 investigators from a range of relevant disciplines. The PDRAs will establish the necessary infrastructure in terms of web site, software development environment, and collaboration tools. Together with the named investigators, they will consult with the whole community on software requirements. Some software is available from the applicants, and some from other UK groups. The PDRAs will write additional programs, scripts and workflows as necessary, although we stress the aim is not to replicate existing programs but rather ensure their optimum use. The areas to be covered include single particle reconstruction, helical reconstruction, tomography, and electron crystallography.
In addition, there will be strong links to the macromolecular crystallography community through the involvement of CCP4, and the NMR community through CCPN. These established collaborations provide useful experience for the development of a CCP in cryo-EM. In addition, we will look specifically at bridging the gap between these techniques in order to support multi-disciplinary studies, for example by facilitating data transfer. We will also liaise with the Electron Microscopy Data Bank in the areas of validation, deposition and annotation.

Planned Impact

In the international research community, there is widespread interest in using EM to tackle big challenges, such as molecular machines in action and membrane complexes in situ. The field has strong links to atomic structure methods, especially crystallography, while electron tomography has strong connections to cell biology. The spatial dimension is needed to understand biological networks and machines, and complements traditional systems biology approaches. By supporting EM research groups in the UK and encouraging a collaborative effort, the proposed Partnership will have an impact in all these fields. We will improve the technological platform upon which scientific advances depend by (i) making existing computational tools more robust and useable, (ii) creating new computational tools and workflows where there are gaps identified, and (iii) promoting best practice through dissemination of information within the community.

The Partnership will also have an impact on individual researchers through its training and knowledge exchange aspects. Existing researchers will of course benefit through improved software tools and environment. However, we specifically wish to lower the barriers to entry into the field of cryo-EM. This applies not only to students and young postdocs, but also to researchers moving from other fields or wishing to use cryo-EM as an additional technique. The expansion of EM as an important component in the toolkit for understanding cellular and sub-cellular biology relies on the availability of researchers competant in the computational techniques required to interpret the data. The Partnership will help by rationalising the computations required and by providing training.

The problems being addressed by EM are of major importance in biomedical science, e.g. dynamic systems involving protein folding/refolding/misfolding, important in neurodegeneration and other misfolding diseases, virus-host interactions, and chromatin structure and modification. Although our primary focus in the Partnership is on the fundamental science, advances here ultimately have an impact on translational and medical research. We are focussing on a technique rather than a particular scientific area, so the impact is likely to be very broad.

By uniting the UK cryo-EM community, the Partnership will also have an impact on the strategy for future development. By acting together, the UK cryo-EM community will have a stronger voice. This will be used to influence software developers, instrument manufacturers and standards development. They will also be able to provide input for national and international policy makers. As a specific example, the CCP-EM will be well-placed to be an important contributor to the European INSTRUCT infrastructure project in structural biology.

An initiative on EM software for the UK community is totally new, will focus work from the entire UK and will also attract considerable international interest. The Partnership proposal is a modest start but long overdue, and will lead to the establishment of a CCP-EM. This will have a huge impact on the UK and international EM community and will greatly facilitate new work and entry of new labs into this expanding field.

Publications

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Burnley T (2017) Recent developments in the CCP-EM software suite. in Acta crystallographica. Section D, Structural biology

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McNicholas S (2018) Automating tasks in protein structure determination with the clipper python module. in Protein science : a publication of the Protein Society

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Patwardhan A (2012) Data management challenges in three-dimensional EM. in Nature structural & molecular biology

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Wood C (2015) Collaborative computational project for electron cryo-microscopy. in Acta crystallographica. Section D, Biological crystallography

 
Description COST Open-EM
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
 
Description CCP-EM renewal
Amount £1,091,548 (GBP)
Funding ID MR/N009614/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 02/2016 
End 02/2021
 
Description West-Life (Horizon 2020)
Amount € 796,000 (EUR)
Funding ID EINFRA-9-2015 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 10/2015 
End 09/2018
 
Title Volume database for PDBeShape 
Description A database containing high quality volume data for prokaryotic and eukaryotic ribosomes, and class I and II chaperonins, taken from the Electron Microscopy and Protein Data Banks (EMDB and PDB). Entries are annotated with links to external databases such as Pfam/Rfam and NCBI taxonomy. The volume database contains a set of pre-calculated volume/shape alignments determined by a software pipeline SMaSB. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact None yet. 
URL http://www.ebi.ac.uk/pdbe/emdb/pdbeshape/about/
 
Description Leeds EM facility 
Organisation University of Leeds
Department Astbury Centre for Structural Molecular Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution Help to scope computational requirements of the new Electron Microscopy facility. Later, we will help with installation, and writing of custom software pipelines.
Collaborator Contribution Advice on software required by Electron Microscopy facilities. This advice was included in a grant application submitted in February 2016, as well as informing on-going plans.
Impact Material for inclusion in the CCP-EM renewal grant application, concerning the software infrastructure needs of cryoEM facilities. Election of Neil Ranson (Leeds) as Deputy Chair of CCP-EM. Leeds hosted a Relion workshop in September 2016.
Start Year 2015
 
Description eBIC collaboration 
Organisation Diamond Light Source
Department Diamond
Country United Kingdom 
Sector Academic/University 
PI Contribution eBIC (electron Bio-Imaging Centre) at Diamond Light Source provides scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for single particle analysis and cryo-tomography. As part of CCP-EM, my group are providing computational support to users of eBIC, in the form of installing software and direct assistance. We benchmark certain key codes, and have optimised their usage on Diamond compute clusters. We plan to co-develop software pipelines to enable users to get rapid feedback on their data collection.
Collaborator Contribution eBIC provides a pool of cryoEM users who can provide feedback on the developing CCP-EM software suite, and provide test datasets. Diamond staff will also help to co-develop software pipelines for rapid feedback.
Impact The collaboration involves hardware development (microscope and computational resources), application software development, and structural biology. We maintain a set of EM software on Diamond systems, available to users of eBIC. We have benchmarked version 2.0 of the Relion software on a GPU platform at Diamond. We have helped with the installation of cryoSPARC at Diamond.
Start Year 2015
 
Title CCP-EM software alpha release 
Description CCP-EM intends to distribute an easy-to-install software suite containing tools for cryo-EM. At present an alpha-release for developers is available. Note that it requires building from source and installation of some dependencies. 
Type Of Technology Software 
Year Produced 2015 
Impact Feedback from collaborators on the software framework. This will help to develop the final release for end users. 
URL http://www.ccpem.ac.uk/download.php
 
Description CCP-EM Spring Symposia 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Annual community meeting for biological electron cryo-microscopy. Raised profile of CCP-EM and had first meeting of the consortium management group "Working Group 1". Attendance has increased each year, and we can now attract high profile international speakers. The 2017 event is in conjunction with the official opening of the eBIC facility at Diamond. The next Spring Symposium is planned for April 2018 at Keele University. Talks from the Spring Symposia are now published as a special issue of Acta Crystallographica section D. The talks are also live-streamed and available afterwards as videos, to increase the impact of the event.

Some feedback on CCP-EM activities, guiding current direction.
Year(s) Of Engagement Activity 2015,2016,2017
URL http://www.ccpem.ac.uk/training/spring_symposium_may15/spring_symposium.php
 
Description CCP-EM Twitter account 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Twitter account to provide updates on CCP-EM itself, and also general news of interest to our community.To March 2018, we have made 185 tweets, and have 789 followers..
Year(s) Of Engagement Activity 2015,2016,2017
URL https://twitter.com/ccp_em
 
Description CCP-EM community meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact There was a general discussion of priorities for CCP-EM, which resulted in a list of activities/tasks to be pursued.

A couple of lab visits arose from contacts made at this meeting.
Year(s) Of Engagement Activity 2013
URL http://www.ccpem.ac.uk/courses.php
 
Description CCP-EM website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The CCP-EM website is used for dissemination of the aims of CCP-EM, advertising our meetings and workshops (as well as 3rd party meetings of interest to our community), and distributing software.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
URL http://www.ccpem.ac.uk
 
Description Dynamo training course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact CCP-EM hosted a training course on Subtomogram averaging with Dynamo in December 2015. The course helped with the professional development of scientists in cryoEM. It also helped to raise the profile of CCP-EM as the main consortium for cryoEM in structural biology.

A second edition of the Dynamo tutorial workshop was held on the Harwell campus on 28th-29th November 2017. The course was attended by 25 students.
Year(s) Of Engagement Activity 2015,2017
URL http://www.ccpem.ac.uk/training/dynamo_dec15/dynamo_course.php
 
Description Instruct Workshop: Computational tools for combining atomic and volume data 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Training of students and postdocs in academia and industry on latest algorithms and software.

Developers from crystallography were inspired to look more at lower resolution EM data.
Year(s) Of Engagement Activity 2015
URL http://www.ccpem.ac.uk/training/instruct_apr15.php
 
Description Relion training course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation workshop facilitator
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The first one-day training course on Relion was held at Diamond Light Source on Thursday 16th October 2014. It focussed on both theoretical and practical aspects of the RELION software package and was led by the principle developer Dr Sjors Scheres (MRC-LMB), with help from Felix Weis (MRC-LMB) and the local CCP-EM team. A second one-day course was run on 8th December 2014.
The course was held for a 3rd time in Leeds on 19th September 2016. This course was used to introduce the improved GPU-enabled version 2 of Relion. There was also a tour of the new cryoEM facility at Leeds.
These courses have always been heavily over-subscribed, reflecting the rapid expansion of the field of cryoEM. These courses have also been attended by staff from pharmaceutical and biotechnology companies, who are now looking to include cryoEM in drug discovery pipelines.

This has helped the UK cryoEM community understand the Relion software, so that it can be applied in their research.
Year(s) Of Engagement Activity 2014,2016
URL http://www.ccpem.ac.uk/courses.php
 
Description Talk at BCA meeting 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact I was advertising CCP-EM to an audience of crystallographers. It helped to inform them of the state of the art in cryoEM.

None
Year(s) Of Engagement Activity 2015
 
Description Talk at Liverpool June 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The talk covered cryoEM in general and CCP-EM to a mixed audience of biologists. The talk sparked several questions in the talk, and enquiries afterwards.

None.
Year(s) Of Engagement Activity 2015
 
Description Tutoring at CEITEC Winter School on Structural Cell Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave talks on "De novo protein modelling and its use in interpreting experimental structural data" and "Volume data from cryoEM and crystallography: fitting and building atomic models and matching against other volume data". These sparked questions from the students and discussions with other tutors.

I invited my host at CEITEC to give a talk at the CCP-EM Spring Symposium later that year.
Year(s) Of Engagement Activity 2015
 
Description the annual Icknield workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The first Icknield Workshop on Model Building and Refinement for High Resolution EM Maps was held at the RAL / Diamond campus, Harwell, UK on 2nd - 4th March 2016. The course was aimed at structural biologists with high resolution EM maps ready for / in the process of modelling, building and refinement. This three day course hosted some of the leading software developers and provided ample contact time to allow delegates to discuss their data in detail alongside traditional lectures and tutorials.

This is now an annual event, with the second instance being held in April 2017. The next installment is due to be held in May 2018.
Year(s) Of Engagement Activity 2016,2017
URL http://www.ccpem.ac.uk/training/icknield_2016/icknield_2016.php