Description of Work

Proposal 505977

European Macromolecular Crystallography Infrastructure Network 2

MAX-INF2

 

 

1. Project Summary

The main goal of this network is to address the teaching of macromolecular crystallography (MX) by organising workshops and schools for the European MX community. MX is essentially a physical science, and since more and more research groups with a biological or medical background are embarking on crystallography experiments, the need for teaching the basic principles of protein crystallography, e.g. X-ray data collection and structure determination, analysis and exploitation, is growing.

Furthermore, this network will act to disseminate knowledge concerning the development of the hardware and software required by the MX community in Europe. Crystal structure determination of proteins, nucleic acids and their complexes relies heavily on research infrastuctures such as synchrotron radiation (SR), as well as hardware and software development projects. It is proposed to have a forum for identifying areas of cooperation centred around the exploitation of SR, hardware and software development in life science crystallography and extending the software coordination currently centred on the highly successful British CCP4 project to a European base. Many macromolecular crystallographers, in academia and the pharmaceutical industry, support the network described in the current application, and it can be seen as the successor of the highly successful Human Potential network MAX-INF (record number 19468). MAX-INF2 brings together large-scale facilities, hardware and software developers, academic and commercial users to reflect the current requirements of high throughput macromolecular structure determination in the post-genomic era.

 

2. Overall description and fundamental objectives of the CA

2.1 Description of how the CA will enhance the services provided

MX is a significant and expanding component of the European biological and medical research programme. Structural genomics, i.e. the high-throughput determination of crystal structures of biological macromolecules on an organism- or disease-wide basis, is a new and rapidly expanding area of MX. The large number of structural genomics projects currently in operation world-wide clearly show the interest in and importance of structural biology, in particular MX. Of paramount importance for future success in the public and private sector is the training of the next generation of macromolecular crystallographers. MAX-INF2 will provide a mechanism for organising and funding meetings, workshops and schools in MX in Europe. It is aimed to promote cooperation on infrastructure, hardware and software development, and to act as a focus to attract research groups and individuals moving into this area of research by providing appropriate training.

The network will provide a solid basis for MX in Europe mainly not only by teaching crystallography, but by serving as an information and integration network. The emphasis of the network is on the coordination of ongoing research efforts rather than the actual funding of research. MAX-INF2 will thus organise a series of meetings, workshops and schools, as well as setting up a website for information exchange. The latter will enhance the contacts between the different software and hardware developers (many of whom are based at synchrotron radiation sites). However it will, equally importantly, enhance interactions between the developers, the SR sites and the user community. Implementing these activities and assessing their success will involve extensive consultation with users, both informally through workshops and schools and more formally through the Web site.

One major deliverable of the integrating activities is a more cohesive user-friendly research environment, which will improve access to the SR infrastructures for the MX community. The existence of an increasing number of SR beam lines for MX data collection means that better coordination of the software available at those sites (e.g. graphical user interfaces for data acquisition and MX software to take the user ever closer to on-line analysis of the structure at the SR site), requires systems that are common to the sites or at least make the differences more transparent to the user. It is important to have an integrated approach between hardware, data collection facilities at synchrotrons and software, as well as to take account of feedback from user groups, especially when the automated structure determination protocols required by structural genomics efforts become more prevalent. The SR providers will benefit enormously from the educational aspects of the network, since a community of well-trained and well-informed users will be created. Currently SR providers face a heavy workload of user support when user groups visit their facilities, due to the non-standard nature of the user interfaces. Much of this workload will be relieved by the integration activities to be undertaken by the network and by the aforementioned training of users.

Integration of software under the GUI as provided by the CCP4 suite is a further means to integration. This aim is dependent on the willingness of network members to integrate their software under the umbrella of a GUI, but there are big benefits to users if cooperation can be agreed.

In summary this network will spread good practice, common protocols and collaboration within the field of crystallography in Europe.

2.4 Ethical and gender issues

No special ethical or gender issues are raised by the proposed CA.

3. List of participants

Table 1 - List of participants of the CA

 

Participant number

 

Organisation

(name, city, country)

 

Short name

 

Date enter project

 

Date exit project

 

Short description (i.e. fields of excellence) and specific roles in the consortium

1

Max-Lab, Lund, Sweden

Max-Lab

Start of project

End of project

Synchrotron site, (hardware development), coordinator

2

SRS, Daresbury, UK

SRS

Start of project

End of project

Synchrotron site (hardware development), CCP4 software development, website development. Participate in N2, N3 and N4

3

EMBL, Hamburg, D

EMBL-HH

Start of project

End of project

Synchrotron site (hardware & software development) Participate in N2, and N3

4

ESRF, Grenoble, F

ESRF

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

5

EMBL, Grenoble, F

EMBL-G

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

6

University of Vienna, Vienna, Austria

Vienna

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

7

Paul Scherrer Institut, Villigen, CH

PSI

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

8

Soleil, Gif-sur-Yvette , F

Soleil

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

9

Diamond, Chilton, UK

Diamond

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

10

Freie Universität Berlin, Berlin, D

FUB

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

11

Anka, Karlsruhe, D

Anka

Start of project

End of project

Synchrotron site (hardware development)

Participate in N2 and N3

12

York University, York, UK

York

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

13

Universiteit Leiden, Leiden, NL

Leiden

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

14

Nederlands Kanker Instituut, Amsterdam, NL

NKI

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

15

Georg-August-Universität Göttingen, D

UNIGOE

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

16

Uppsala Universitet, Uppsala, SE

Uppsala

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

17

CERBM-GIE, Strasbourg, F

CERBM-GIE

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

18

MRC, Cambridge, UK

MRC-LMB

Start of project

End of project

MX laboratory, Software development

Participate in N2 and N3

19

ITQB, Lisbon, P

ITQB

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

20

Universita di Pavia, I

Pavia

Start of project

End of project

MX laboratory, User

Participate in N1, N2 and N3

21

FORTH, Heraklion, GR

FORTH

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

22

A. Mickiewics University, Poznan, PL

AMU

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

23

University of Copenhagen, Copenhagen, DK

UKBH

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

24

Biovitrum, Stockholm, SE

Biovitrum

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

25

Astra Zeneca, Macclesfield, UK

Astrazeneca

Start of project

End of project

MX laboratory, User

Participate in N2 and N3

26

IRBM, Pomezia, I

IRBM

Start of project

End of project

MX laboratory, User

Participate in N1, N2 and N3

 

 

4) List of activities

Table 2 - List of activities of CA

Activity Number

Descriptive Title

Short description and specific objectives of the activity

1

Management of CA

2

Coordination meetings

Organisation and management of the activities of the network, and ensure that the work of the network is disseminated to the scientific community.

N1

Schools

Biannual large scale methods-based Schools with around 200 participants, including many students and young scientists. Talks will be based around methods development.

N2

Workshops

A series of small workshops, with around 25-40 participants, providing hands-on experience in defined topics of methodology, including data collection, refinement, molecular replacement, MAD, automated model building etc.

N3

Integration workshops

Forum for coordination, information and discussion between hardware/software developer and users and to allow further integration of synchrotron data collection facilities, detectors and software for structure determination..

N4

Website

Repository for network-related documents, and to provide the community with a single point of reference for schools and workshops organised by the network

 

5) Financial information

INSERT TABLE A3.1

6) Estimated breakdown of the EC contribution per reporting period

INSERT TABLE A3.2

 

7) Management of the activity

7.1 Description of the activity

Management of the Network

The network is modelled on ongoing collaborative efforts within MAX-INF and benefits from the high level of experience gained within that project. Participant 1, the coordinator, will be supported by participants 2, 12 and 19. Computing support for establishing and updating WWW pages will be provided by a band 5 programmer at Daresbury Laboratory (participant 2).

Coordination meetings

Annual coordination meetings for the administration of the network will be organised, and there will be provision for extraordinary meetings if the need arises: the latter may comprise relevant subgroups of the total members. These meetings are separate from the "Integration Workshops" in activity N3, as the latter are forums for internal scientific discussion rather than administration. A total of 5 meetings are planned in the 5 years of the contract. It is important to arrange a meeting early in the first and at approximately equal intervals thereafter. However, the actual timing needs to be flexible, and will aim to address the needs of the network, and to coordinate with other meetings of interest to the members. The date and venue of each meeting will be decided at the previous meeting. All members of the network can propose scientific workshops that they would like to organise.

Each coordination meeting will follow an agenda typically including the following items:

The organisation of each meeting will comply with the following rules:

The meeting will decide

Decisions will be taken on a simple majority basis. Any changes to the above organisation of the coordination meetings or to any other aspects of the network organisation will have to be approved by a 75% majority. Every participant has one vote.

The financial organisation of the network is as follows (see aappendix 1 for budget):

All finances will be administered by LU; however only the management finances are direct funding to LU. The remainder will be distributed as outlined below (1)

Travel reimbursement for travel associated with attending the coordination meeting will be paid to the participants at the time when they travel to the Coordination Meetings (2) (15000/year)

The participant who organises the Methods School will receive the funding (50.000) for this activity during the particular year that the School is held (N1). The participant responsible for organising this school will be decided at the Coordination Meeting.

Participants who organise workshops will receive funding. The particular workshops to be funded, the organisers for each workshop and the level of funding each workshop will receive will be decided at the yearly Coordination Meetings (N2) (60.000/year)

The participant to organise the Integration Meeting in a given year will receive the appropriate funding (25.000). This participant will be decided by the Coordination Meeting (N3).

 

7.2 Plan for using and disseminating knowledge

The goal for MAX-INF2 is twofold. The first part involves teaching of macromolecular crystallography in Europe by organising workshops and teaching schools. The importance of the workshops and schools is clear. The MX community is expanding fast, leading to an increasing number of inexperienced infrastructure users who require training at a state-of-the-art level. Previous experience has shown that SR infrastructure operators gain immensely from organising and teaching at the workshops and schools, since in the end they benefit from well-trained synchrotron users who can carry out optimised experiments with less supervision. In addition to transfer of knowledge from the experienced to the inexperienced, the workshops bring together the most experienced providers in a field, generating collaboration and discussion at the highest level.

The second goal is to coordinate research efforts in European laboratories involved in developing methods for MX. This connects the European synchrotrons that provide facilities for data collection with laboratories involved in hardware and software technologies. In order to guarantee a feedback to the user community several different user groups are Participants. The potential benefits of the integration activities are very high, both for participating infrastructure facilities and for other participants. The same advantages apply as for the Schools: enhanced contact between providers and users, and indeed between those concerned primarily with hardware developments at the facilities with those working in software developments to exploit the resulting data.

In order to keep informed on further developments within the field of crystallography and infrastructures, MAX-INF2 will keep close contacts with other EC networks or proposals such as BIOXHIT or the I3 IA-SFS ("Integrating Activity on Synchrotron and Free Electron Laser Science"). There will be contact with European scientific societies: members of the MX Special Interest Group of the European Crystallographic Association (ECA) will be informed about the outcome of the coordination meetings in order to facilitate coordination of workshops etc.

The specific emphasis on MX in MAX-INF2 will result in significant added value for the EU and associated economic area, as the structural information on biological macromolecules produced by MX in the academic and private sectors is the motor for major economic developments in the pharmaceutical and biotechnology sectors. Many of the skilled MX practitioners in the private sector have extensive academic training to doctoral level and above, and many have participated in and/or benefited directly from the previous network MAX-INF. MAX-INF2 is complementary to the BIOXHIT and I3-SRS networks: BIOXHIT revolves around technology development for European structural genomics and the educational component of BIOXHIT is focused on practical workshops in specific aspects of structural genomics rather than the fundamental crystallographic methodology (of benefit to all MX practitioners) to be disseminated within MAX-INF2. I3-IA-SFS covers all aspects of research using synchrotron radiation with little specific emphasis on MX as far as education is concerned. The HERCULES course ("Higher European Research Course For Users Of Large Experimental Systems"), which is partly funded by I3-IA-SFS, also offers a very broad education in all aspects of synchrotron radiation; thus it has negligible overlap with MAX-INF2.

The existing website for MAX-INF will be continued and regularly updated. It will act as a repository for network-related documents, and to provide the community with a single point of reference for the MAX-INF2 schools and workshops.

 

8) Description of the other activities of the CA

8.N1 Activity N1: Schools

8.N1.1 Description and objectives of the activity

The objective of this activity is to spread good common practice in MX techniques at the theoretical level. Theoretical Schools in the methodology of MX will be thus be organised every two years. These will be mainly lecture-based, which differentiates them from the practical workshops described in activity N2. The schools will encourage good practice, common protocols and collaboration by educating the practitioners of MX in the latest methods. The schools will be based on a model successfully used in MAX-INF and will probably be held at Villa Olmo in Como, Italy. They will involve up to 200 participants, including many students and young scientists. The participants will not be limited to members of the consortium but they will come from EU member states. The MX community is large and these larger-scale meetings are essential to give the opportunity to a significant proportion of this community to hear about advances in techniques and to ensure that EC MX groups are operating at an internationally competitive level. Talks will be based around all aspects of methods development in the MX area, and will be presented by a combination of international scientists, infrastructure facility operators and software and hardware developers, mostly members of the consortium. In addition young scientists (Ph.D. students and postdoctoral fellows) will be encouraged to present their results to a wide forum, discuss limitations of the infrastructure and indicate areas in which they feel developments are required.

8.N1.2 Participants in the activity

The Methods Schools will be organised on each occasion by one of the Italian participants (20 and 26) in cooperation with one of the non-Italian participants. In the first year the organisers are participants 14 and 26. The theme and participants will be as described in section 8.N1.1. On the subsequent two occasions, the organisers will be decided at a previously held coordination meeting.

8.N1.3 Outline implementation for the full duration of the activity (including milestones and deliverables)

As the deliverable in this case is dissemination of knowledge and techniques in the field of MX, the school is a milestone and deliverable in itself.

 

Year 1

Year 2

Year 3

Year 4

Year 5

deliverable

Methods School

 

Methods School

 

Methods School

 

 

8.N1.4 Expected outcome

The school will result in a raised level of education and awareness in the theoretical and methodological aspects of MX. The schools will encourage good practice, common protocols and collaboration. This will produce more skilled practitioners in the discipline, which is of general benefit, ensuring increased competitiveness for European MX research groups.

8.N2 Activity N2: Teaching workshops

8.N2.1 Description and objectives of the activity

The objective of this activity is to spread good common practice in MX techniques on the practical level. Teaching workshops will allow young scientists to be coached by specialists in the latest techniques and methods. Therefore MAX-INF2 will organise a series of small workshops, with around 2040 participants, on defined topics in methodology, including, but not limited to:

The participants will be young scientists (Ph.D. students and postdoctoral fellows). They will not be limited to members of the consortium but they will come from EU member states. The workshops will be organised by members of the consortium, in particular those involved in the development of new methodologies or the synchrotron radiation providers. The workshops will differ from the Schools described in activity N1 by being very much "hands-on", i.e. practical more than theoretical. Three to four workshops a year will be held, on different topics and at different sites, to cover the needs of the rapidly expanding and widespread MX community. The organisation and selection of workshops will be comparable to those organised in MAX-INF (see Appendix 1 for previous organised workshops). The choice of workshops for a given year is dependent on ongoing developments in the field and will be decided at MAX-INF coordination meetings after application from consortium members to arrange such workshops (see section 7.1). In the first year the CA plans to finance workshops arranged by participants 7, 8 and 19.

8.N2.2 Participants in the activity

All participants (126) are welcome to arrange workshops and to apply for funding for these at the coordination meetings. Those who have done so in the past (i.e. in the framework of MAX-INF) are participants 210, 12, 1415, 1719 and 22.

B.N2.3 Outline implementation for the full duration of the activity (including milestones and deliverables)

 

Year 1

Year 2

Year 3

Year 4

Year 5

deliverable

34 workshops

34 workshops

34 workshops

34 workshops

34 workshops

 

 

8.N2.4 Expected outcome

The workshops will have a very similar outcome to N1, except that here the emphasis is on practical skills, thus the workshops will have particular importance for the synchrotron service providers, where practical abilities in data collection and structure solution are of prime importance in an era where these processes can be carried out in hours rather than months or years as previously. In this respect such workshops are of particular importance for the integration of MX activities in Europe. It has also been experienced during MAX-INF that such workshops are fertile ground for the exchange of scientific ideas between the organisers and teachers, i.e lateral transfer of information occurs as well as vertical (from teacher to student).

8.N3 Activity N3: Integration Activities (Integration Workshop)

8.N3.1 Description and objectives of the activity

The competitiveness of MX in Europe is crucially dependent on the exchange of scientific ideas between methods developers, synchrotron radiation providers and representatives of the user community, which is the objective of activity N3. There are many aspects of infrastructure provision for MX that will benefit from a culture of cooperation. The integration workshops are a good starting point for collaborations and exchange of ideas, which in this case is mainly horizontal rather than vertical in the cases of the Schools (activity N1) and practical workshops (activity N2).

These workshops will take place over approximately one and a half days. The venue for meetings will be one of the participating infrastructure facilities (participants 15, 7 & 10), on a rotating basis. All attendees will be notified of the date and place at least four months in advance. In the integration workshops presentations on new developments from hardware and software developers will be given. Furthermore, in the MAX-INF2 integration workshops there will be presentations of the activities at each synchrotron with sufficient time for discussion and questions. There will be approximately 5070 participants at each integration meeting: one or two delegates representing each of the 26 members of the network. Invited speakers from outside the network will always be invited, in order for the network to obtain information on developments elsewhere. The majority of participants will be at the group leader/senior researcher level, providing a wealth of expertise. These workshops will be used to identify additional common developments and MAX-INF2 will provide funds to ensure that these developments progress, e.g. by providing infrastructure to facilitate communication. This aspect has been highly successful in MAX-INF, e.g. with the developments in the DNA project.

Another aim will be to extend the UK-based CCP4 model of cooperation to software development in the European community. There is already a critical mass of software development as represented by the CCP4 suite of programs, which is used extensively around the world. The CCP4 suite is a collection of programs donated by many people working on methods and code development. A Graphical User Interface (GUI) has been developed within CCP4 which provides the opportunity for further integration of software from the perspective of the user, without removing the independence of individual software suppliers. The GUI provides an excellent framework within which further cooperation between European software developers can take place, and wider development and exploitation of the GUI will be addressed by the network, directed at high throughput MX.

 

8.N3.2 Participants in the activity

All participants (126)

8.N3.3 Outline implementation for the full duration of the activity (including milestones and deliverables)

 

Year 1

Year 2

Year 3

Year 4

Year 5

deliverable

 

Integration Workshop 1

Integration Workshop 2

Integration Workshop 3

Integration Workshop 4

8.N3.4 Expected outcome

This activity will produce a heightened awareness of the activities of other network participants. This will lead to more effective hardware and software development and avoid unnecessary duplication of effort due to ignorance of current trends. The presence of user representatives (both academic and industrial) will ensure that the information is quickly disseminated to the user community, as well as enabling rapid feedback into the development process.

 

8.N4 Activity N4: Web site

8.N4.1 Description and objectives of the activity

Macromolecular crystallographers already use the Internet and electronic communication extensively, and these are the chosen media for dissemination of information in MAX-INF2. The MAX-INF web site was set up (www.ccp4.ac.uk/maxinf) to act as a repository for network-related documents, and to provide the community with a single point of reference for schools and workshops organised by the network. An email distribution list has also been set up to co-ordinate network activities. These activities will be continued and developed in MAX-INF2. The web pages are generated by PHP scripts which allow a degree of automation. In particular, network members can upload information to the web site through simple form-based interfaces. New interfaces will be added as required. The web site will act as a forum for integration activities (N5). If there is sufficient demand, a "Wiki" will be set up for discussion of integration activities, as has been done for other projects (www.ysbl.york.ac.uk/ehtpx). Specific links to the home pages of the participating members will be established and the outcome will be a network of centres, or a "virtual centre", a resource easily accessible by all macromolecular crystallographers in Europe. Programming support will be provided by existing CCP4 staff at Daresbury Laboratory (participant 2).

8.N4.2 Participants in the activity

Participant 2

8.N4.3 Outline implementation for the full duration of the activity (including milestones and deliverables)

 

Year 1

Year 2

Year 3

Year 4

Year 5

Deliverable

Functioning web site

Maintenance of web site

Maintenance of web site

Maintenance of web site

Maintenance of web site

8.N4.4 Expected outcome

The web site will smooth the functioning of the coordinating activity and will therefore enhance the productivity and expected outcomes of activities 13. It will also function as an information point for the whole MX community in Europe, informing about the latest technical and methodological developments as well as the currently available workshops and schools.

Appendix 1 Proposal budget MAX-INF-2

Participant

Activity

Item of expenditure

Amount/year

Amount Total

1

1

Management

9 000

45 000

For all participants

2

Coordination meetings.

Travel costs for representatives of all consortium members

15 000

75 000

For participants organising N1

N1*

Como meeting

55 000

165 000

 

of which:

Travel subsidies for speakers and young scientists from consortium members

25 000

 
   

Rent Villa Olmo and services

25 000

 
   

Specific secretarial effort for organising workshop

5 000

 

For participants organising N2

N2

Total 3 to 4 workshops/year

65 000

325 000

   

1 Workshop

17 500

 
 

of which

Travel for tutors and organisers

10 000

 
   

Costs for educational tools (eg. rent computers for tutorials)

5 500

 
   

Specific secretarial effort for organising workshop

2 000

 

For participants organising N3

N3

Integration meeting

25 000

100 000

 

Of which:

Travel and accomodation costs for representatives of consortium members

21 500

 
   

Costs for secretarial effort for organising workshop

3 500

 

2

N4

Programmer

0

0

         

Totals

     

720 000

* We plan to organise 3 Como meetings in 5 years, hence 3 x55000 = 165000

We plan to organise 4 integration meetings, hence 4 x 25000 =100000

Anastassis Perrakis, NKI Amsterdam
Elena Conti, EMBL-Heidelberg
Victor Lamzin,EMBL-Hamburg
Klaus Scheffzek, EMBL-Heidelberg