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Second Report of the International Advisory

Board (IAB)

Chairman: Professor Bertil Andersson

Review: March 2017 Report submitted: August 2017

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Contents 1. Introduction 3 2. Background 5 3. Global Context 7 4. Major Challenges facing SciLifeLab 8 5. Governance and Structure 10 6. Research Infrastructure – Platforms 12

6.1 General 12 6.2 Drug Discovery 14 6.3 Bioinformatics 15

7. Research and National Research (Flagship) Projects 18 8. Non-biomedical Life Sciences (environment, 19 Biodiversity, agriculture & forestry) 9. SciLifeLab Fellows Programme 20 10. SciLifeLab Faculty 23 11. Research Integrity 24 12 . Human Resources 26 13. Branding 26 14. Innovation and Industrial Collaboration 27 15 Clinical Collaboration 28 16. Need for Coordination 29 17 Future Reviews 30 Appendices

1. IAB Visit Programme 08/09 March 2017 2. List of participants during the IAB meeting 3. IAB membership 4. Members of the SciLifeLab Governing Board 5. Summary of Recommendations from the IAB Report 2015 6. Explanation of Figure 1 – Organisation Diagram (Note by Director) 7. Site Management of SciLifeLab at Solna (Note by Director)

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1. Introduction Since the first report of the International Advisory Board - IAB (then termed the Strategic Advisory Board) in February 2015, there have been significant changes in governance and management and senior personnel coupled with further reviews of platforms and infrastructures at the SciLifeLab. There have been changes within the SciLifeLab governance as well as significant changes in the senior personnel of SciLifeLab itself. Chairmanship of the governing board has passed from Professor Göran Sandberg (K & A Wallenberg Foundation) to Professor Carl-Henrik Heldin, Uppsala University. The membership of the Governing Board itself has changed in the past two years and its membership is given in Appendix 4 The founding Director of SciLifeLab, Professor Mathias Uhlén, has stepped down although he remains active in SciLifeLab science through his continuing work on the Human Protein Atlas and as the Royal Institute of Technology (KTH) Integration Director. The other founding Co-Director, Professor Kerstin Lindblad-Toh, from Uppsala University has also stepped down to continue her work on the genomics of domesticated animals. A new Director, Professor Olli Kallioniemi, has been appointed after an international search process, with Professor Lena Claesson-Welsh, from Uppsala University, becoming the new Co-Director. In addition, the post of Infrastructure Director has been created with Dr Annika Jenmalm-Jensen, Karolinska Institute (KI) as its first incumbent, together with Scientific Directors from Uppsala University (UU), Stockholm University (SU), KI and KTH. Together these form the SciLifeLab Management Group. In addition, there have been changes in the leadership of the four host universities. At the Karolinska Institute –KI there is an Interim Vice-Chancellor, Prof. Karin Dahlman-Wright, who will be succeeded by Professor Ole Petter Ottersen, currently Rector of Oslo University; and Professor Sigbritt Karlsson has recently taken over as the President of Royal Institute of Technology – KTH. Professor Astrid Söderbergh-Widding continues as Vice –Chancellor of Stockholm University as does Professor Eva Åkesson as Vice-Chancellor of Uppsala University.

Figure 1: New structure at SciLifeLab (the Director’s explanation is given in Appendix 6)

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In addition to the IAB recommendations in 2015, there have been a number of further reviews, including one external review conducted by the Swedish Research Council (VR) and SciLifeLab’s own evaluation of the platforms, in which some IAB members participated. These have resulted in changes to governance and to operations. Since the previous IAB review, there has been a substantial change in the governance, management and operational structures of the SciLifeLab. These are very much aligned with the IAB recommendations from 2015 and the IAB welcomes these changes. The IAB is also pleased that, in response to the IAB’s previous recommendations, a new mission and vision statement has been formulated. During this period there have been a number of other reviews of elements of SciLifeLab’s operations, including a review of the Drug Discovery Platform Given all these changes, the IAB Chairman considered it best to defer the planned second meeting of the IAB from September 2016 until the first part of 2017 to allow these modifications time to settle in before the visit. The timing is also opportune as the Swedish Government has presented a new Research Bill in which changes relating to research and higher education will have an impact, both on SciLifeLab and on its hosting universities. The Bill addresses increased academic/industrial links and related matters including a possible revision of tenure rules for university faculty. Also, it formally defines the SciLifeLab as one of the country’s national research infrastructures, similar to, for example, the MAX IV national synchroton laboratory in Lund. The members of the IAB are very much committed to the concept of the SciLifeLab as Sweden’s forefront activity in empowering molecular life sciences, one on which much international attention is fixed. This enthusiasm and commitment is also shown by the involvement of several members in the various platform reviews that have taken place. It is a further measure of their commitment that all but one (due to a long-standing pre-commitment) of the IAB members were able to take part in the 2017 meeting. At this point the IAB wishes to record its thanks to Professor Carl-Henrik Heldin, to Professors Olli Kallioniemi and Lena Claesson-Welsh and to all their colleagues involved in our review meeting. It particularly wishes to thank the administrative staff at both Stockholm and Uppsala for the excellence of the visit arrangements and for their hospitality as well as for their clear and informative presentations. The IAB thanks the four university heads who came together as a group to meet us for a full and open discussion and thanks the Rectors for addressing many of our concerns from the first report. The IAB also thanks Ms Karin Schemkel, from the Ministry of Education, who took time out from her busy schedule to meet the IAB and provide background information about overall science policy in Sweden, including in relation to the SciLifeLab, and information about the new Research Bill.

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The IAB also wishes to thank the SciLifeLab Fellows for their engagement with the International Board in discussing various important issues affecting them as well as their input about the SciLifeLab itself.

2. Background It is worth recapping the origins of the SciLifeLab, as this has created a ‘legacy’ in terms of governance, structure and organisation on which the IAB comments later. Basically, SciLifeLab is financed through a number of separate funding lines – SFO (see below), national research infrastructure funds, including a separate budget for the Drug Discovery Platform, user fees and, separately, external grants from VR and the K & A Wallenberg Foundation and other funding sources. The three major Stockholm universities (KI, SU and KTH) together and Uppsala University (UU) had initially responded successfully to a national strategic research funding opportunity (SFO - Strategiska forskningsområden) in the area of molecular life sciences. To consolidate this success and building on the expertise that had developed in the region, SciLifeLab started in 2010 as a collaborative initiative from all four universities in the ‘greater’ Stockholm region (“Mälardalen”) with the SFO funds remaining under the control of each of the individual founding universities. Therefore it was a major strategic research initiative to which national infrastructure funding was later added plus support designated by the Government following the decline of the pharmaceutical industry in the area. SciLifeLab evolved into its role as a national infrastructure centre with a different funding line in 2013 and, has been designated under the new Research Bill to be a major research infrastructure alongside the substantial investments in Max-IV and the ESS located in Lund. However, its origins are very much as a research centre and research, based on SFO money, remains at its core. The SFO funding has been augmented by national research infrastructure funding as well as by PI-led external research support from the Swedish Research Council (VR) and the K & A Wallenberg Foundation. Individual grants from competitive European funding and similar sources support specific research activities. The question then arises as to how this multiplicity of funding (represented by major block grants and the traditional individual project grants) can be best managed through the four universities and the SciLifeLab governing board. The SciLifeLab Board has a complex structure as it is formally responsible to the KTH Board. KTH is the primary host university with the overall responsibility for national funding (as well as the Stockholm part of the SFO funding) accountable to the Ministry of Education. The Board approves the scientific, technical, and administrative/financial content of SciLifeLab’s annual reports with the KTH Board formally approving and relaying it to the Ministry. The SciLfeLab Board does not have a legal personality, hence the KTH Board acts in this role. These complex roles are also represented in the nomination of the Board members. The Chair of the board and the industry representative are appointed by the government. The four host universities appoint one member each, formally agreed by the KTH board. The three remaining members are suggested by the non-host universities in Sweden and, after consultation among the host university Rectors, the KTH Board formally appoints them.

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The structure and funding are shown in Figures 2 and 3 below. This shows that the operations are equally divided in terms of funding between infrastructure support and research programmes.

Figure 2: Structure of the SciLifeLab and funding, illustrating the multiple funding sources (mixed economy) of SciLifeLab funds

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Figure 3: Financial overview for 2016 showing sources of funding for SciLifeLab. It should be noted that SciLifeLab benefits from ‘in-kind’ support from the universities, e.g. salary support of the SciLifeLab Faculty

3. Global Context Molecular life science is one of the most rapidly developing areas of scientific and technological endeavour involving many disciplines. It now ranks as one of the major research areas in science alongside materials science (nano-) and computer sciences, including artificial intelligence. Advances in this area have had a revolutionary effect on the understanding of biological processes, on biomedicine and healthcare, pharmaceutical science, agriculture and forestry, and as a basis for environmental sciences and sustainability. Molecular life sciences and biomedicine have become major components of research endeavours in the major economies and have become ‘big science’ going well beyond the support capacities of individual institutions Significant funding is now being devoted to research in this area as witnessed by the creation of the Broad Institute in Boston, MA, a partnership between Harvard University and MIT, and the Francis Crick Institute in London, a partnership between Cancer Research UK, the UK MRC and Imperial College, King’s and University Colleges London). What is happening is that the life sciences is changing so that, in addition to smaller Principal Investigator (PI) - driven programmes, there are now large inter-disciplinary teams bringing together critical masses of expertise in order to push further the frontiers of knowledge. These large teams focus on answering big questions which provide both a rich environment for individual PIs and are increasingly necessary to address the important questions in biology and medicine. Therefore, research structures have changed in recent years with the formation of

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major institutes such as those in Boston and London and the SciLifeLab has to be viewed, necessarily, within that context. As an advanced economy, Sweden needs to retain a forefront position in molecular life sciences. The ‘greater’ Stockholm region (“Mälardalen”) represents a very significant concentration of expertise and investment, both academic and industrial. However, in recent years, the industrial sector has declined in part due to external market forces. SciLifeLab is a major initiative of national significance and its operations need to be optimised to maintain the competitiveness of Sweden and “Mälardalen” in this rapidly evolving area (that goes beyond the individual institutions), so as not to lose the benefit of the very significant public (and private) investment already made.

4. Challenges facing the SciLifeLab – much progress achieved but further steps are needed

The IAB regards the SciLifeLab to have been a very visionary initiative by the four founding universities. It congratulates the SciLifeLab and its Board for the significant advances already achieved. Because of the various funding sources supporting the SciLifeLab, its funding and management are necessarily complicated reflecting this situation. The IAB views SciLifeLab in a very positive light given its achievements to date. The SciLifeLab founders, supported by the Swedish system, have to be warmly congratulated for their foresight in funding this crucial scientific area. The four universities, and their leaderships, in particular, are to be highly commended for coming together to create this collaborative structure. SciLifeLab is a product of its complex institutional origins and its various funding streams, all of which have contributed to its complex legacy. Whilst congratulating SciLifeLab and its founders for what has been achieved to date, in the opinion of the IAB, decisive further steps have to be taken if SciLifeLab is to advance to fully exploit its potential in sustaining academic and industrial progress. In fact, SciLifeLab is now at a critical ‘fork in the road’ in its evolution and several major questions have to be resolved, including how best to synergise the various sources of SciLifeLab funding. SciLifeLab is still striving with its identity. Is it a collaborative research initiative between the four hosting universities, or is it a national infrastructure provider, or is it a national institution? The multiplicity of possible roles may be summarised as SciLifeLab having a ‘dual role’ between that of being a platform and infrastructure provider to enable largely external PI-led projects and that of being an advanced research institute with its own major research programmes on par with similar other internationally recognised institutes. Added to this is the complexity of its administrative structure and legal status. The IAB considers that, in order to increase clarity for all concerned, the SciLifeLab Board should better define the overall objectives of the SciLifeLab and the means of achieving them.

1. SciLifeLab is a major strategic initiative and its operations need to be optimised to maintain the competitiveness of Sweden and “Mälardalen” (Greater Stockholm) region in molecular life sciences.

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The SciLifeLab was built on the SFO funds aimed at fostering strategic research. It has since grown into a national infrastructure provider and has added a pharmaceutical research activity, through the Drug Discovery Platform. It now has a mandate as a national research infrastructure providing a service to the whole Swedish bio-science community. This needs to be combined with an advanced research programme (for which the SFO funds were dedicated), integrating the complementary expertise of its four host universities with its own SciLifeLab faculty and fellows in a unique environment. This will enable it to go beyond the individual founding institutions to become a world leading research institute combined with a national infrastructure service mission in the spirit of the new biology. If SciLifeLab concentrates only on its infrastructure mandate, then the IAB considers that, without the stimulus of high-level research programmes, there will be a gradual decline in the intellectual capacity which is essential to keep the infrastructure platforms at the international cutting edge. This would be a significant lost opportunity for research in Sweden, particularly as many research groups in Sweden are small and relatively insular. The IAB notes that, in response to its previous recommendation, SciLifeLab has produced a new vision and mission that has been formulated to bring together its two branches of both infrastructure provision and research as advocated by the IAB. This move is to be warmly welcomed as it does address the dual and mutually reinforcing role and personality of the institution. In this way, SciLifeLab can start to compete with the likes of the Broad and Crick Institutes, the Sanger Centre (UK) and similar centres, usually university-based, in Europe and elsewhere. Taking this line means, from the IAB perspective, that there must be an even tighter collaboration, integration and consolidation between the four university ‘parents’ in the context of SciLifeLab. This will require an increased coordination at all levels within these institutions, not only at the most senior levels. Thus, SciLifeLab has to be recognised as going beyond the capacity of an individual university in assembling a critical mass of complementary expertise and combining it in novel and forward looking ways. It then follows that the governance, leadership and senior management of SciLifeLab must to be empowered to deliver this objective whilst remaining accountable to the partner universities and to the funders. These are key issues which the SciLifeLab Board should discuss and address. The coming together of the four universities, originally and especially over the past two years has been commendable. Therefore, the IAB does not see, a priori, that there should be a separate legal structure for SciLifeLab. However, if the universities are unable to take the further steps necessary in terms of integration in support of SciLifeLab in a timely manner, then the creation of the SciLifeLab with its own legal personality needs to be considered by the SciLifeLab Board as the only way forward. The IAB feels that there is urgency in this matter. The international standing of SciLifeLab will depend on it, and on an efficient and visible research programme that is clearly associated with SciLifeLab, to be developed within the next two years.

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5. Governance and Structure In response to our previous recommendations, the SciLifeLab Management Group has suggested a new vision and mission statement, which the IAB endorses. This states that the SciLifeLab vision is to be a national hub for molecular life sciences with a mission:

• to provide unique and enabling infrastructures for high-impact molecular life science research;

• facilitate internationally leading collaborative research in a community of excellent scientists;

• and promote translation of biomolecular research findings into lasting societal benefits.

However, having now established a new operational model, the IAB considers this to be a new baseline from which SciLifeLab has to advance further if it is to consolidate its success so far and reach new levels of achievement The IAB congratulates the leaderships of the four hosting universities for coming together, following the successful bids for SFO funds by the Stockholm Universities and, separately, by UU which led to the creation of SciLifeLab. We also commend the increasing commitment and involvement of the four Rectors in support for and the operations of SciLifeLab. There are now regular meetings between them and the SciLifeLab Board Chair, the Director and the Co-Director, and this is to be commended. This response to the IAB recommendation for such closer leadership involvement is very welcome. However, the IAB considers that having taken these major steps in creating a much more unified operation, there is now a need to take further steps towards a more complete and necessary integration. Following a major review of SciLifeLab by VR in December 2015, it was agreed to change the relevant statute to ensure that the Board had a clear role in the organization, governance and long-term financing of SciLifeLab. It also recommended that while SFO funds should continue to go through the individual universities the use of such funds should be brought together to a much greater degree than hitherto in a dialogue and in partnership between the SciLifeLab Board

2. The IAB advocates the combined model of both national infrastructure

provider and major research centre in order to fulfil the new vision and mission statement and to enable SciLifeLab to compete with forefront international centres in Europe and elsewhere

3. However, if the universities are unable to take the further steps necessary

in terms of integration in support of SciLifeLab then the creation of the SciLifeLab with its own legal personality remains the only way forward.

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and the founding universities. This should result in a far greater coordination and increased synergy between the institutions and SciLifeLab. The first step was the change from having two distinct nodes in Stockholm and Uppsala to having an integrated arrangement although facilities continue to be located at the two sites. This is a welcome development. The IAB warmly commends the steps that have been taken over the life of SciLifeLab to increase coordination, collaboration and efficiency. However, to reach the next step of forefront international competitiveness, it is necessary for this process be continued and intensified.

Figure 4: New SciLifeLab governance to be operational as from August 2017 In response to the recommendations from the various reviews, a new governance structure is being put into place in 2017 as shown in Figure 4 above. As will be seen from the VR review recommendation, SFO funds are still directed to each university under SciLifeLab committees that also involve an ‘Integration Director’ who is a senior faculty member in each university. The IAB understands that the legal documents regarding their exact responsibility and functions are still being defined in a process that is planned to be ready by summer 2017. The SciLifeLab Director has stated that this is a critical process in that the details largely dictate how much of SciLifeLab is governed by the national board, and how much by the SciLifeLab committees at each University, as well as how the SciLifeLab management group can coordinate these activities. The top level of the universities’ management is very engaged and coordinated. This coordination and engagement needs to be further developed at all levels. Therefore,

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the IAB welcomes the appointment of the four Integration Directors. They need to be further empowered in their roles so that they have much greater visibility and authority within their respective institutions. Despite these welcome reforms, some significant problems remain and where further coordination between the various parties needs to be intensified. These include the ability of SciLifeLab to be able to deal directly with external parties, both with industry, health care organisations and in respect of international scientific collaborations, and in the effective management of funds, personnel, space and material resources by the SciLifeLab Board and the Director. Furthermore, there is a need for a much better alignment between the universities, especially in relation to some of the Departments, and their involvement with

SciLifeLab. This extends to having common appointment and tenure procedures with respect to SciLifeLab Fellows (see below) and a common approach to innovation procedures and practices with respect to SciLifeLab as well as in the area of research integrity.

6. Research Infrastructure 6.1 Platforms - General

The rather complex infrastructure platform structure was the subject of an international evaluation in 2016 recommended by the IAB. The IAB welcomes the significant progress made in reviewing and reforming and simplifying the platforms. The evaluation of the platforms included several IAB representatives (Jan Ellenberg, Yoshihide Hayashizaki, Sirpa Jalkanen, and Jonathan Knowles). It looked at existing platforms and evaluated proposals for new initiatives which has resulted in

4. There should be increased coordination between the four universities not only at the Rectors’ level but at all levels (including Departmental Heads and other faculty levels) to support SciLifeLab’s mission.

5. The IAB considers that the possibility of having formal agreements between the

universities to enable one university (presumably KTH) to be in a position that it can rapidly endorse such matters as agreements between SciLifeLab with industrial partners or to sign international research collaboration memoranda without undue delay or bureaucracy is an important matter for consideration by the SciLifeLab Board.

6. There has to be more devolved authority for the senior management (under the

SciLifeLab Board), with the Director having greater control of personnel issues, finance and physical space and laboratories.

7. There needs to be common policies, procedures and decisions with regard to

appointment and tenure procedures (SciLifeLab Fellows), to innovation procedures and practices and to ensure research integrity.

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consolidation together with the introduction of new platforms. The new platforms were presented to the full IAB. They and their associated facilities (with funding sources) are shown in Figures 5 and 6 (below). The IAB commends the SciLifeLab governance and management for implementing the outcome of these reviews that has reduced and simplified the number of platforms (including satellite platforms – national platforms located outside the Stockholm – Uppsala region) and linked the facilities to platforms in a clear manner. In so doing, SciLifeLab has removed its regional facilities and this has resulted in a single-layered and simplified structure. Platforms have to be seen to be open to the community at large in a transparent process. The platforms tend to work independently of one another in ‘silos’ while, at the same time, there is overlap between the platforms. This is not necessarily a bad thing. However, there is a tendency for the platforms to see themselves as somewhat separate entities within the SciLifeLab. They must be seen unambiguously to be core parts of the SciLifeLab programme. The responsibility of the Platform Directors needs to be further clarified and they should be accountable to the Director SciLifeLab. The role of the Infrastructure Director is an important part of this structure. In relation to operational infrastructure and the added value of the platforms, it would be useful to understand how the platforms interact. Therefore, it would be useful to perform an analysis of which projects use multiple platforms and develop strategies to facilitate access to multiple platforms by one user/project. These data would form the beginning of a “Venn diagram” or possibly an informative ‘interactome figure” of the interactions between the SciLifeLab platforms. For the future and to plan for a steady evolution of the platforms the IAB welcomes the establishment of life cycle planning in a transparent and simplified system. This requires an ongoing programme of peer reviews and evaluations.

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Figure 5: New Platform organisation Despite some progress in this direction, there still appears to be a lack of a prioritisation in terms of access to platforms. Therefore, the IAB recommends to the SciLifeLab Board that there should be a merit-based prioritisation system including a special provision for access to platforms by SciLifeLab Faculty and Fellows, whose regular usage will keep the platforms at the cutting edge and align SciLifeLab’s research and service activities. If possible a similar ‘access process’ should be used for all platforms, with one integrated web portal, allowing a single application for multiple platforms.

Figure 6: New Platforms and associated facilities. Purple represents facilities that are also KAW funded, Blue represents those that receive VR funding and Red represents new facilities starting in 2017.

6.2 Drug Discovery Platform As mentioned earlier, this Platform was created, largely, in response to the loss and move of AstraZeneca and Pharmacia from the region. It was subject to a review by international experts in 2016 as part of the infrastructure evaluation, the outcome of which was positive. From the IAB perspective, there are several matters which still require to be addressed. In particular, the programmes appeared to be focused on potency, with relatively little focus on drug-like properties of small molecules required for in vivo testing and

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clinical studies. This means that the Platform may be much less productive than would be the case if other modern approaches were to be taken. Drug discovery in an academic setting can be very productive and advantage needs to be taken of the critical intellectual mass provided by the SciLifeLab and its community. There should be renewed focus on new classes of therapies, peptides, proteins and nucleic acids that fit well to academic centres and now start to show superior properties. There is considerable activity in this area throughout the world, including in academia, and, therefore, SciLifeLab should develop a distinctive and different perspective so as to create something exceptional rather than replicating the industrial technology of the last century. This will be one of the areas on which the IAB will focus at its next meeting.

6.3 Bioinformatics Sweden has built a strong national bioinformatics infrastructure that compares favourably to other countries. In many ways it is unique and represents a competitive advantage. A new comprehensive description of the integrated national structure for bioinformatics has been put in place and the SciLifeLab efforts play a significant role nationally. Since the last IAB the Bioinformatics Platform has been restructured (shown in Figure 7). The IAB acknowledges that there is a diversity of funding streams in the national model and recognises that organizational complications will ensue. The IAB sees the continuing need for an assured longer term funding commitment that would ease planning in this rapidly evolving area. This would allow Sweden to further maintain competitive advantages from its unique model that addresses bioinformatics needs at many levels. The Bioinformatics platform should engage more with its users in pre-award grant phases, including interfaces to funding agencies. This is relevant for original project design, for data management plans but also for financial planning. It would be good practice to include for costs for the bioinformatics in such awards. A preventive effort that avoids underpowered studies, with inadequate bioinformatics investment, would be beneficial.

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Figure 7: The SciLifeLab Bioinformatics Platform The platform should have a clearer interpretation of the concept “Heterogeneous data” and how such data is processed and linked together. For example, chemical biology data were handled separately from other data, yet are clearly related to other types of molecular data. The platform needs to establish a “data roadmap”. The contributions of the technical bioinformatics researchers is sometimes not adequately acknowledged in publications and the “reach-through” model for authorship for the Bioinformatics platform was unclear to the IAB. The IAB found that the platform had an unclear strategy when it came to facilitating and organizing re-use of data generated in one project in other projects. Projects were handled separately and in a somewhat “siloed” manner. This is, potentially, a missed opportunity in Sweden, in particular, where data can be extensively linked. It may be good to develop a clear strategy for the data generated by the platforms and the tools to access them and their re-use. This should tie in with the overall attitude to stewardship for SciLifeLab data.

The IAB could clearly appreciate the competences of the bioinformatics platform in genomic medicine efforts. However, it was unclear where the SciLifeLab’s responsibilities and the mission ended, in particular, within genomic medicine in relation to actual patient treatment. There should be a clear division of responsibilities separating data analysis, diagnostic classification and handling of incidental findings. The presentation did not include a clear strategy around over- and under-diagnoses for example.

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The logic of charging for short-term support but not for long-term support in WABI, was unclear to the IAB. In the longer term, maybe a joint application to the Wallenberg Foundation for both support services could be planned. It was difficult for the IAB to understand the hardware infrastructure and what is the long term plan for it. Again, this is a potential threat to the competitiveness of the platform. The supercomputer needs, the relationships to other national efforts, e.g. SNIC should be part of the SciLifeLab strategic plan.

8. Platforms should be open to the community at large, with a transparent, merit-based prioritisation process and with a special provision for access for SciLifeLab Faculty and Fellows. The IAB recommends to the SciLifeLab Board that there should be a provision of approximately 20% of the total SciLifeLab resource to these ‘internal’ users (both Fellows – highest priority - as well as Faculty) who, beyond this allocation, would bid for open access alongside other users within the national infrastructure provision.

9. Platforms should be, unambiguously, core parts of the SciLifeLab programme and

should report and be under the general direction of Director, SciLifeLab. 10. SciLifeLab should perform an analysis of which projects use multiple platforms, with the

data forming a “Venn diagram” to show the added value and links of SciLifeLab platforms and provide easy mechanisms for cross-platform access.

11. The IAB endorses the SciLifeLab plan for a steady evolution of the platforms with the

establishment of life cycle planning in a transparent and simplified system, with an ongoing programme of peer reviews and evaluations.

12. The IAB will focus on the Drug Discovery platform at its next meeting 13. There needs to be a continuing need for an assured long term funding commitment for

the Bioinformatics platform. 14. SciLifeLab needs to develop a clear strategy for the data generated by the platforms

and the tools used to access and re-use data in line with overall data stewardship policies (FAIR).

15. There needs to be a clear and rational charging logic within the Bioinformatics Platform

for short-term and long-term support – at a later stage a joint application to the Wallenberg Foundation for both support services could be undertaken.

16. A long-term plan for the Bioinformatics Platform hardware should be part of SciLifeLab

strategy.

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7. Research and National Research (‘Flagship’) Programmes As stated earlier, the life sciences are undergoing a rapid revolution into ‘big biology’ coupled with the still prevalent smaller PI-led investigations which remain very important. Therefore, research cannot just be single PI-led. Worldwide, life sciences are changing with major initiatives dependent on the assembling of critical masses of interdisciplinary expertise, the use of major infrastructures, access to well-developed databases and the creation of synergies with other disciplines and competences. In the previous report, the IAB recommended the establishment of more flagship (national research) programmes within the SciLifeLab portfolio. These would take advantage of the existing service platforms or develop new ones, coupled with availability of data and research infrastructures, to address ‘grand challenges’ in the life sciences. The IAB considered that the Human Protein Atlas could be seen as an excellent example of such a programme that can be said to represent “big biology” – one of the few in Sweden. The IAB noted that there has been limited progress in developing such programmes since the previous review. However, the IAB notes that the management of SciLifeLab is in discussion about the possible development of research proposals which could be developed into major national programmes and this is welcomed by the IAB. Such programmes should be driven by the SciLifeLab Fellows and Faculty from the four founding universities leveraged on the SFO funding and in concert with other Swedish expertise. A useful model and past example is that of the Human Protein Atlas developed by Matthias Uhlén The IAB continues to recommend the development of such major research projects, which are of national interest, and which take advantage of the Swedish data infrastructure and the national investment in the SciLifeLab in terms of both facilities and brainpower. The criteria for such projects should be that they aim for high impact research for life science community combining both a top down approach with bottom-up involvement and they should be collaborative endeavours. SciLifeLab must be the fulcrum around which such projects are initiated, being the coordinator and the ‘data coordination centre’. Major national research projects may also be seen in an international context in which Sweden and SciLifeLab can lead in developing international consortia. During the review meeting, the IAB received presentations on Genomics Medicine Sweden, and on the Human Cell Atlas, both of which had potential to become major projects. However, the IAB did not give deep consideration to topics that could form such major national programmes. The IAB had recommended that there should be renewed efforts to promote environmental life sciences, biodiversity, agriculture, and forestry studies within the SciLifeLab activities. This is very necessary given the importance of the agricultural

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and forestry sector in the Swedish economy. This continues to be an area that is under-represented and needs to be encouraged and given priority. In developing future national research (“flagship”) projects, SciLifeLab has to engage with some of the funders such as VR, the Wallenberg Foundation and the Science Academies in their foresight activities for science planning as well as performing its own analysis and scoping studies. Based on the platforms and infrastructure facilities, it should develop a Strategic Research Plan aligned with its vision and mission statement. SciLifeLab is the ideal place for such an approach and should take a leadership position in responding to Grand Challenges, working with and encouraging the whole Swedish academic sector but especially the critical mass in molecular life sciences that is in the greater Stockholm region. To accomplish this, SciLifeLab has to develop high-level processes for evaluating proposals for national projects through a ‘bottom-up’ call within the host and other universities based on assembling critical masses. The IAB anticipates that SciLifeLab Faculty and Fellows will have a particularly important role to play in such projects and they should be involved in proposals as commensurate with their own research interests.

8. Non-biomedical Life Sciences – environment, biodiversity, agriculture and

forestry The environmental life sciences in Sweden has an enviable reputation with a very high citation rate. While one might assume that, with full, assured and equal access

17. The IAB continues to recommend the development of major national research projects, which are in the national interest, and take advantage of the Swedish data infrastructure and the national investment in the SciLifeLab in terms of both facilities and brainpower.

18. Such national projects may also be seen in an international context in which

Sweden and SciLifeLab can lead in developing international consortia. 19. In developing future major research projects, the SciLifeLab Board should

engage with the funders such as VR, the Wallenberg Foundation and the Science Academies, in their foresight activities for science planning and should develop its own Strategic Research Plan to clarify the near-term and long-term visions and mission priorities.

20. The SciLifeLab Board should develop processes for evaluating proposals for

national research projects through a ‘bottom-up’ call within the host and other universities based on assembling critical masses with SciLIfeLab Faculty and Fellows being involved.

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to SciLifeLab, the result would be more projects spanning the life sciences, but this has not been the case. In its first report the IAB recommended that efforts should be made to encourage a greater non-biomedical life sciences uptake and continuing efforts are required to achieve this outcome. In the SciLifeLab, biomedical life sciences continue to dominate and creates a critical mass in this area. Calls for major national research projects could be used to stimulate the non-biomedical life sciences combining top-down encouragement with a bottom-up response. Again, the work on domesticated animals led by Kerstin Lindblad-Toh is an example.

9. SciLifeLab Fellows Programme Sweden does not have a particularly strong tradition in the recruitment of international faculty and faculty antecedents are strongly national and local. The IAB is very impressed and commends the initiative taken to have a very high-level recruitment of young investigators originating from the most prestigious institutions from around the world. Encouraging them to start their academic careers in the greater Stockholm region has resulted in an important influx of high-level human capital. Thus, the SciLifeLab Fellows form an elite cohort of very bright young brains at the SciLifeLab, spending the bulk of their research time there. The high level of SciLifeLab recruitment is demonstrated by their ability to win ERC Starting Grants and similar prestigious awards, which recognise their ability and potential. Such a cohort is unique for Sweden and needs to be valued and nurtured. However, their recruitment systems were variable, a result of the legacy of the four institutions acting separately from one another. One institution (KI) had a broad open call while the others had more focused calls. The Fellows themselves are formally appointed as tenure track assistant professors on a 4year (+2) contract (paid for from SFO funding) within one of the four universities and are expected to be involved in the activities of whichever home department they have been assigned to in the host university. While in some universities, the Departments have been involved in recruitment, this has not always been the case. In contrast, the SciLifeLab leadership and management team have not been involved in the process of recruitment of SciLifeLab fellows. Thus, in Stockholm, it has been difficult for the SciLifeLab

21. Environmental life sciences, biodiversity, agriculture and forestry continue to be an area that is under-represented and needs to be encouraged and given priority.

22. Calls for major national projects in the non-biomedical life sciences could be

used to stimulate this area by combining top-down encouragement with a bottom-up response.

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leadership and management team to step in to support the working conditions and mentoring of fellows at specific departments. The Fellows would benefit from more clarity at the start of their engagements with regard to their positions both in the universities and in SciLifeLab. The latter is their research base but there may have been unforeseen delays and obstructions in starting which, in several cases, had eroded their tenure track period. The Fellows themselves had come together in a ‘self-help’ group, and had produced a SWOT analysis and presentation illustrating their concerns when they met the IAB. In discussions with the IAB, the Fellows really highlighted their commitment and passion to their science and to the SciLifeLab as well as speaking of the challenges which they had encountered. With regard to the issue of space allocation, criticism could be made as to why the SciLifeLab Director could not resolve such space problems and access to basic facilities. The IAB was informed that the Director has no direct authority over space allocations within the SciLifeLab space, as the laboratory is a tenant of the building in Stockholm that it occupies (jointly operated by the three Stockholm universities) – see Appendix 8. It is not acceptable for the Director of a prestigious research operation, such as SciLifeLab, to be put in this position and again illustrates the urgent need for the parent Universities to act as one and support the SciLifeLab management. Another issue which the SciLifeLab Board should address is that the Fellows have no prior right of access to the platforms and infrastructure and so must ‘wait in line’ with all applicants, or do not obtain access to the service of their home institution in line with their research needs. One can understand this approach strictly in terms of fairness to access of a national infrastructure. On the other hand, Sweden has invested in recruiting this elite cohort and it makes sense to exploit their potential by providing them with an element of regulated but preferential access, otherwise, why would such bright young scientists choose to pursue their careers at the SciLifeLab? Again, this raises the question as to the role of the SciLifeLab in balancing national infrastructure access needs with its role as a forefront research institute. The Fellows, together with the SciLifeLab Faculty (see section 11), form the core of SciLifeLab as a research institute. Thus, the question arises as how to arrange a priority allocation of SciLifeLab resources to both sets of users. The IAB recommends that there should be a provision of approximately 20% of the total SciLifeLab platform access to these ‘internal’ users. Beyond that, both Faculty and Fellows would bid for open access alongside other users within the national infrastructure provision. The IAB encourages SciLifeLab Board to consider introducing an EMBL Interdisciplinary Postdocs ‘EIPOD’-like competitive open post-doctoral fellowship scheme, in which a project and a post-doc are jointly supervised by a two PIs, each with a different complementary skill (e.g. wet and dry). This could be an international programme across the SciLifeLab to encourage interdisciplinary research and provide excellent training for the researchers of the future. Tenure track rules are different between the universities so that there may be unequal treatment within the cohort. Furthermore, the tenure track is of a limited

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four-year duration, due to Swedish employment regulations. Therefore, it is difficult to extend tenure in the light of the delays experienced at the start of the appointment. The IAB recommends that the Fellows’ appointments should be the six-year norm that applies in most other parts of the world. The IAB heard that the Swedish Government will develop legislation within the current Research Bill to change tenure provisions on a single national standard but this will be too late to help the Fellows now struggling with the system. Action will be needed to resolve this perceived issue otherwise the SciLifeLab may lose to the opportunity to benefit from this elite cohort of young researchers. As far as tenure review is concerned, the IAB strongly recommends that the Rectors appoint a single, common tenure committee for the SciLifeLab Fellows which can apply commonly agreed criteria and whose decisions will be accepted by the constituent institutions. Also, consideration should be given to whether a common appointment committee is also necessary. The Fellows are of the opinion that they have been largely left without sufficient mentorship, especially guidance on how to operate within the Swedish research system, how to develop research and data management planning, and how to best exploit the Bioinformatics Platform. In 2015, the IAB said that there is a vital need for academic and research mentorship that is especially important for younger and international recruits. A procedure for this should be developed as a high priority. This is particularly important for foreign recruits who may not be familiar with the Swedish academic research system. It is unfortunate that this has not yet happened to any great extent and the IAB recommends that an Academic Senior Research Coordinator be appointed for the Fellows programme. This person should be a reputable senior scientist with a passion for mentoring within and outside his/her own disciplinary interests. This role will also have responsibility for ensuring that the Fellows operate with best research conduct especially with regard to research integrity, ethics and data practice. IAB advises that there should be coordination with the Wallenberg Foundation Fellows in the Life Sciences as there is much to be gained by mutual exchanges between the two groups. In fact, the IAB had addressed some of these issues in its previous report saying that the career prospects of recruits need to be factored into the less than flexible Swedish employment system. This has to be done while retaining flexibility in terms of human resources management while, at the same time, developing the tenure prospects of the younger recruits. To achieve this, these young recruits need to be given some teaching opportunities – but only to a limited extent to avoid distraction from their main mission: ground breaking research at the highest international level. In summary, the IAB recommends that the SciLifeLab Board should work together with the four hosting universities to coordinate both the recruitment of Fellows and to introduce a common process for promotion and tenure assessment. This is a small but elite cohort of researchers who need to be treated flexibly rather than follow the detailed processes, which may apply in any individual institution. The IAB considers

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that such a dialogue between the SciLifeLab Board and the universities would be beneficial to all parties.

10. SciLifeLab Faculty SciLifeLab faculty is a much larger group of PIs than the fellows, and comprises faculty of the four host universities whose research interests are such that they spend at least some of their research time within the SciLifeLab conducting molecular life sciences research. In some ways, this could be considered to be a very substantial ‘in kind’ contribution by the universities to the research output of SciLifeLab. There are significant differences in the way in which SciLifeLab faculty are designated in Solna and Uppsala. In the former, they are faculty who have chosen to commit themselves to spending their research time in the SciLifeLab building while, in Uppsala, faculty respond to an opportunity to be part of both the SciLifeLab and their departments for research purposes. Thus, there is no harmonisation between the sites with respect to the SciLifeLab faculty. This reflects the origins of SciLifeLab and the differences between Solna and Uppsala,

23. The IAB recommends to the SciLifeLab Board and to the host Universities that

the Fellows’ appointments should be the six-year norm that applies in most other parts of the world with special action needed to resolve the dilemma faced by current Fellows due to start-up delays.

24. The IAB strongly recommends to the SciLifeLab Board that the Rectors appoint

a single, common appointment and tenure committee for the SciLifeLab Fellows which can apply commonly agreed transparent criteria and whose decisions will be accepted by the constituent institutions.

25. The IAB recommends to the SciLifeLab Board that a Senior Research

Coordinator be appointed for the Fellows programme. The appointee should develop procedures for senior mentorship of SciLifeLab Fellows as a matter of high priority.

26. The IAB strongly recommends to the SciLifeLab Board and to the host

Universities that there has to be a coordinated approach to the recruitment policy regarding Fellows. who should be at the core of major national programmes. In addition, it is recommended to develop a national science framework for their tenure prospects and to embed their own research interests and meet the strategic needs of the overall programme.

27. The IAB encourages the SciLifeLab Board to consider introducing an EMBO -

‘EIPOD’-like competitive post-doctoral fellowship scheme, in which a project and post-doc is jointly supervised by a two PIs, each with a different complementary skill (e.g. wet and dry). This could be an international programme across the SciLifeLab to encourage interdisciplinary research and provide excellent training for the researchers of the future.

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corresponding to the previous structure for SciLifeLab with two separate nodes. In Stockholm, the Solna building is the home base for SciLifeLab for KTH, I and SU faculty. In contrast, in UU, SciLifeLab activities have taken place mostly within existing departments and a decision was made to open SciLifeLab to all interested faculty based on applications and expressions of interest. SciLifeLab management is now planning a new faculty definition, with the goal to harmonise the faculty definition. This could involve two types of faculty, including both "in-house” as well as remote (associated) members from both host and non-host universities. This will be dependent on setting up new criteria for faculty, taking into account future developments. The IAB would wish to encourage a clear and common definition to be applied to such faculty without, however, having it too rigid or narrow. This is because such people represent a very visible cohort of SciLifeLab committed people within their own institutions and this helps with overall visibility and should assist the Integration Directors in getting the SciLifeLab message across to the rest of their universities. One attraction is the availability of special equipment and facilities and the support which is associated with it. At the same time, together with the Fellows, they form a critical mass necessary for the advancement of SciLifeLab as a research centre and may form the core of future national research programmes. Finally, it represents a saving of resources that need not be duplicated in the four universities. Similar to the Fellows, once defined in a consistent manner, SciLifeLab faculty raises the question of the need for a priority allocation of SciLifeLab resources to both sets of users. Both form the core of SciLifeLab as a research centre. The IAB recommends to the SciLifeLab Board that there should be a provision of approximately 20% of the total SciLifeLab resource to these ‘internal’ users. Beyond that, both Faculty and Fellows would bid for open access alongside other users within the national infrastructure provision.

11. Research Integrity Having high standards of integrity and sound ethical practice is a sine qua non in research. This requires operating with exemplary best practice. While ultimate responsibility for research integrity lies with each individual researcher, institutions must also take responsibility. The life sciences, generally, and biomedicine, in particular are areas of research endeavour in which research integrity has been much discussed due to major instances of misconduct. In addition, the non-reproducibility of much of the data

28. There should be some form of common definition of SciLifeLab Faculty without this being too rigidly or narrowly defined and who, with the Fellows, have priority access to the Platforms.

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reported (estimated at around one third of all research results) has become a key issue. Given the focus on biomedicine within ScIlfeLab, the topic of research integrity within SciLifeLab has to be of high priority. Recent high profile cases at two of the host universities reflect the importance of this issue for SciLifeLab. Thus, no one within the SciLifeLab ‘circles’ should be unaware of these issues and the importance which has to be attached to the promotion of best research practice within the Laboratory. While responsibility for response to allegations rests with the employing institution, there is high reputational risk for SciLifeLab should the research have been conducted within SciLifeLab. Therefore, it is necessary that SciLifeLab management engages with the employing institutions to ensure that all those conducting research in SciLifeLab have had appropriate training in integrity, research ethics and the responsible conduct of research. Furthermore, in line with best practice elsewhere, provision has to be made for data management planning, data collection, storage and archiving. There has to be some form of quality control in terms of the design of experiments and data collection in order to address the reproducibility issue. The IAB was pleased to note that data management planning, data collection, storage and archiving are the responsibility of the PI and the long-term storage of data is the responsibility of the Universities concerned. However, in order to help and support the users, their host Universities, as well as the SciLifeLab platforms in this respect, SciLifeLab has set up a Data Office. This office is independent of the Bioinformatics Platform, but closely collaborating with it. The IAB recommends that a protocol be established between SciLifeLab and the four host universities that can ensure that researchers have appropriate education and training and that there are robust and commonly agreed procedures for investigation should incidents occur. Such protocols can be extended to the researchers using SciLifeLab facilities from other universities and from collaborating organisations. The aim has to be the promotion of the best research practice at all times. Furthermore, SciLifeLab needs to designate a senior person as its Research Integrity Officer.

29. It is necessary that SciLifeLab management engages with the employing institutions to ensure that all those conducting research in SciLifeLab have had appropriate training in integrity, research ethics and the responsible conduct of research. Therefore, the IAB recommends to the SciLifeLab Board that a protocol be established between SciLifeLab and the four host universities to ensure that researchers have appropriate education and training and that there are robust and commonly agreed procedures for investigation should incidents occur.

30. Provision has to be made for data management planning, data collection, storage

and archiving. The ongoing efforts of SciLifeLab of both the Bioinformatics Platform and the SciLifeLab Data Office need to be reinforced as a matter of priority.

31. Such protocols should be extended to the researchers using SciLifeLab facilities from other universities and from collaborating organisations.

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12. Human Resources

In the previous report, the IAB stated strongly that human capital (expert staff) is at the core of the SciLifeLab success and needs to be nurtured to ensure continuing success. The IAB had been particularly concerned that the staff working on platforms and infrastructures had to stay up to date and see a well-developed career progression ahead of them, accompanied by professional training structures. The IAB saw this as vital for the continuing health of the technological platforms and facilities and for the recruitment of well-qualified staff. The response to the recommendations was that this is to be encouraged but, as the staff are employed by the host universities, the role of SciLifeLab management is limited and HR policies are not within its mandate. Again, this is another example of some of the problems of the present structure and emphasises the need for common standards to be applied between the universities with the full involvement of SciLifeLab senior management and the SciLifeLab Board should address this issue.

13. Branding

SciLifeLab is now recognised on the national and international stage. Previously, we were looking at comparisons with the Broad (USA) and Francis Crick (UK) Institutes. This remains the case and one cannot take these other models to be followed exactly by SciLifeLab. Each has been created within its own national structural and economic environment so that the Broad is a partnership of Harvard University and MIT while the Crick Institute is structured as an independent organisation with founding partners from three London universities, the Wellcome Trust and Cancer Research UK. Therefore, SciLifeLab has to take account of its founding framework and build this into a new and more efficient model. SciLifeLab is also approaching a critical point in its development and decisions must be made at this crossroads as discussed above. Future research recruitment should be aimed at achieving this model, and fulfilling the vision and mission statement. Part of this will be the branding to reflect this role. It is appreciated that, as a national facility, including the four universities within the brand could create jealousies from the rest of the country. However, it has to be accepted that the Mälardalen region may be seen as the molecular life sciences hub of the country. At the same time, it has to compete on the global stage both in its output on one hand and in its

32. A coordinated procedure is needed to address career development and related human resource issues especially for the staff involved in platforms and infrastructure service.

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recruitment on the other. Therefore, if the founding universities are seen as a key asset in the SciLifeLab profile then the brand should reflect it. Therefore, the IAB suggest branding SciLifeLab as an entity but linked to the four universities and indicating its role as the national life sciences hub. Such an approach will also serve as strong signal to the international life sciences industry that this is a desirable location with which to be alongside. Another aspect of branding relates to how SciLifeLab supported tools and the data generated may be attributed to the SciLifeLab brand. The IAB considers that branding has to cover all aspects of SciLifeLab activities including the platform and facilities activities.

The IAB notes the steps already taken to promote SciLifeLab. One good example is the collaboration, now in its fifth year, between SciLifeLab and Science magazine to offer prizes to young graduates or graduate students for essays based on their thesis work with four winners in the categories of Cell and Molecular Biology, Ecology and Environment, Genomics and Proteomics and Translational Medicine. SciLifeLab should look at other opportunities to promote its brand not just in Sweden but worldwide. The IAB notes that one such initiative is done in collaboration with Keystone Conferences, alternating between Uppsala and Stockholm. The latest Keystone meeting in Stockholm co-hosted by SciLifeLab on Singe Cell Technology attracted 500 participants. Another possibility could be to hold further major conferences on molecular life sciences, possibly in cooperation with the Nobel and Wallenberg Foundations.

14. Innovation and Industrial Collaboration

33. In terms of branding, SciLifeLab has to take account of its founding framework and build this into a new and more efficient model.

34. IAB suggests branding SciLifeLab as an entity linked to the four universities

and indicating its role as the national life sciences hub. Such branding has to cover all SciLifeLab related activities.

35. SciLifeLab and its Board should look at opportunities to promote its brand not

just in Sweden but worldwide. 36. The existing major Keystone Conferences could be supplemented by other

major conference on molecular life sciences, possibly in cooperation with the Nobel and Wallenberg Foundations.

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Collaboration with industry is to be encouraged and it is necessary that SciLifeLab is really pro-active in this area especially as the new Research Bill is strongly emphasising academia/industrial collaboration. A unified approach is very necessary so that SciLifeLab and its community speak with a single voice to industry. The latter should be invited to be a significant partner in national research projects with companies being encouraged to second researchers to the platforms. Ideas and technology transfer through people is the ideal mode for such collaboration. Again referring to the previous report the IAB had recommended the unification of commercialisation as a single activity or, at the very least, a strong coordination between the host universities. The aim was to promote an efficient means of translating discovery into economic benefit. This has not yet been implemented. While the IAB recognises that, according to Swedish law, the inventor has the right to own IP rights (“lärarundantaget”), a renewed effort is needed to create a system of “Common IP Exploitation”. The IAB recognises that this is not an easy or simple task but it is a very necessary one. This coordination activity would seem to be most appropriately led by KTH as the operating agent for the four universities with respect to the SciLifeLab and the Board has to be pro-actively engaged in promotion of innovation and industrial collaboration. The IAB recommends that the SciLifeLab Board should have a formal and innovative policy for industrial engagement and asks for a paper on this topic to be developed by SciLifeLab management for the Board’s consideration. The IAB wishes to place emphasis on this aspect of SciLifeLab’s work at its next review. One advantage of SciLifeLab having its own legal personality would be that this would make it simpler to create and ‘industrial club’ approach to encourage private sector engagement.

15. Clinical Collaboration

Despite the strong bias of the programmes at SciLifeLab towards biomedicine there appears to be a surprising gap where clinical research is concerned. In the previous report, the IAB stated that “there is a need for a closer interaction between the SciLifeLab and clinicians from the internationally renowned hospitals in Stockholm and Uppsala with the active involvement in the work of the SciLifeLab”. During this

37. The IAB recommends that a formal and innovative policy for industrial engagement is needed and it asks for a paper by SciLifeLab for Board consideration and review. The next IAB review will put special emphasis on industrial collaboration and innovation

38. Industry should be invited to be significant partners in major national research

projects with companies being encouraged to second researchers to the platforms.

39. A renewed effort is needed to create a system of “Common IP Exploitation” which

the IAB recognises as not an easy or simple task but a very necessary one.

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review, we felt that this gap is still apparent and needs to be addressed. This is underscored in the comments above on the responsibilities of the Genomics Medicine efforts. Excitement can be generated in this area with the promotion of cutting edge science merged with the best and most advanced clinical practice. The need for an enhanced effort to create cutting edge research collaborations between the SciLifeLab molecular life sciences and clinicians remains a necessity to move to and remain at the cutting edge of biomedical science. The IAB asks that a paper on this topic be produced for the SciLifeLab Board, in consultation with the IAB. This paper could also address where SciLifeLab research responsibility lies/ends with respect to health service implementation and clinical applications. As with industrial collaboration and innovation, the IAB will put a special emphasis on this aspect of SciLifeLab activities at its next review.

16. Need for Coordination

Throughout this report the IAB stresses the need for increased coordination between the four hosting universities and between them and SciLifeLab These are listed in Table 1 below:

Table 1: List of key coordination areas

40. The IAB asks that a paper on clinical collaboration be produced by SciLifeLab for review by the SciLifeLab Board and the IAB will put a special emphasis on this aspect of SciLifeLab activities at its next review.

• For research integrity a coordinated protocol should be established between

SciLifeLab and the four host universities to ensure that researchers have appropriate education and training and that there are robust and commonly agreed procedures for investigation should incidents occur. Such protocols should be extended to the researchers using SciLifeLab facilities from other universities

• Coordination is needed to address career development and related human resource issues.

• A coordinated approach should be taken with regard to branding.

• A common approach is required with respect to innovation and IP policies.

SciLifeLab: Need for enhanced coordination between the partner institutions and between them and SciLifeLab

• There has to be increased coordination at all levels within these institutions,

not just at the top (Rectors) level, but especially involving Departmental Heads and Faculty.

• There needs to be common policies and procedures with regard to appointment and tenure procedures, to innovation procedures and practices and to research integrity.

• There has to be a coordinated approach to the policy regarding Fellows who have to be at the core of major national programmes and to give a national science framework for the Fellows to embed their own research interests and meet the strategic needs of the overall programme.

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17. Future Reviews The IAB recognises the substantial progress which has been made by SciLifeLab and its governance and management. However, it has identified a number of challenges which it considers that the SciLifeLab needs to address in order to fully exploit the enormous potential of SciLifeLab – its facilities and personnel. The IAB proposes that its next review should be held at the latest by the end of 2018. At that time, it will wish to focus on hearing from users and partners, and the IAB will wish to meet with selected users and partners at that time. The IAB will also wish to examine the triad of relationships: between the universities; between the universities and SciLifeLab; and between university departments and SciLifeLab

41. The IAB proposes that its next review should be held towards the end of 2018 with a significant focus on users and partners.

42. Whilst also addressing such issues as the formulation of national research

(‘flagship’ programmes, the roles of SciLifeLab Fellows and Faculty and areas of concern including the Drug Discovery Platform, linkis with clinical research, development of life sciences areas other than biomedicine and industrial collaboration, the IAB will also wish to examine the triad of relationships: between the universities; between the universities and SciLifeLab; and between university departments and SciLifeLab.

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Appendix1IAB Visit Programme 08/09 March 2017 TuesdayMarch7

ElitePalaceHotel,SanktEriksgatan115,Stockholm18:00 Internal preparation meeting of the IAB, Elite Palace Hotel, Conference room: “Dalasalen”

IAB 19:30 Dinner, Brasseri Norrtull, Sankt Eriksgatan 119 IAB, Director, Co-director, & Chairof the SciLifeLab Board WednesdayMarch8,StockholmSciLifeLab,Tomtebodavägen23,Solna 08:00 Taxi pick-up from Elite Palace Hotel 08:30 Welcome and general information from the chair of the SciLifeLab Board 08:45 Session I: SciLifeLab developments in 2015-2016

IAB, Director, Co-director, Chairman of the SciLifeLab Board, Integration Directors, Management Group, Strategic Relations Officer

- Changes in organization and management: United SciLifeLab concept - SciLifelab under intensive review: main issues arising - New platforms and the life cycle concept of national facilities - Discussion on progress, including previous IAB comments 10:00 Session II: SciLifeLab in 2017-2020 and beyond

IAB, Director, Co-director, Chairman of the SciLifeLab Board, Integration Directors, Management Group, Strategic Relations Officer

- Mission, Vision and Future Strategies redefined - Remaining organizational and management changes

- Key challenges (research programs, faculty definition, fellows/careers, national & society impact)

- Discussion on future strategies 11:30 Meeting with the host university rectors

IAB, Host university rectors (Astrid Söderbergh-Widding, SU; Sigbritt Karlsson, KTH; Karin Dahlman-Wright, KI; Eva Åkesson, UU)

12:00 Lunch & mingle

Invited: IAB, Host university rectors, Director, Co-Director, Chairman of the SciLifeLab Board, Integration Directors, MG, Strategic Relations Officer

12:45 Brief presentation of new platforms (8 x 8 min, plus 7 min discussion each) IAB, Director, Co-director, Infrastructure director, Chairman of the SciLifeLab Board,

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Integration Directors, Management Group, New platform directors 12:45 Introduction by Infrastructure Director 12:50 Platform Presentation: Genomics - Joakim Lundeberg 13:05 Platform Presentation: Proteomics/Metabolomics - Peter Nilsson 13:20 Platform Presentation: Single-Cell Biology - Sten Linnarsson

13:35 Platform Presentation: Chemical Biology & Genome Engineering - Anna-Lena Gustavsson

13:50 Platform Presentation: Cellular and Molecular Imaging - Hjalmar Brismar 14:05 Platform Presentation: Diagnostics Development - Richard Rosenquist Brandell 14:20 Platform Presentation: Drug Discovery and Development - Per Arvidsson 14:35 Coffee Break 15:00 Brief presentation of new facilities (5 x 5 min, plus 5 min discussion each) IAB, Director, Co-director, Infrastructure director, Chairman of the SciLifeLab Board, Integration Directors, Management Group, New platform directors 15:00 Facility Presentation: Ancient DNA - Mattias Jakobsson

15:10 Facility Presentation: Bioimage Informatics - Kevin Smith 15:20 Facility Presentation: Chemical Proteomics & Proteogenomics - Roman Zubarev

15:30 Facility Presentation: Genome Engineering Zebrafish - Johan Ledin 15:40 Facility Presentation: High Throughput Genome Engineering - Bernhard

Schmierer 16:00 Discussion about the fellows program IAB, SciLifeLab Fellows 17:15 Meeting with Karin Schmekel, Ministry of Education and Research IAB, Director, Karin Schmekel 18:00 3 Scientific Highlights (5 min, plus 5 minutes discussion each)

IAB, Director, Co-director, Infrastructure director, Chairman of the SciLifeLab Board, Infrastructure director, Management Group

18:00 Human Cell Atlas project - Sten Linnarsson & Joakim Lundeberg 18:10 Genomics Medicine Sweden initiative - Richard Rosenquist Brandell

18:20 Academically developed cancer drugs entering the clinic - Ulrika Warpman Berglund 18:30 End of Day 1 19:30 Dinner at Stallmästaregården ThursdayMarch9,UppsalaSciLifeLab,Husargatan3,Uppsala 07:45 Taxi pick-up at the hotel

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09:00 Presentation and discussion of the Bioinformatics platform, Data Office and Clinical Bioinformatics

IAB, Director, Co-director, Chairman of the SciLifeLab Board, Infrastructure director, Management Group

09:00 Platform Overview and Support & Infrastructure - Bengt Persson 09:45 Long-Term Bioinformatics Support (WABI) - Pär Engström 10:00 Systems Biology - Thomas Svensson / Jens Nielsen 10:15 Compute and Storage - Ola Spjuth 10:30 SciLifeLab Data Office - Johan Rung 10:45 Clinical Bioinformatics - Valtteri Wirta 11:00 Concluding Discussions 11:20 Recent highlights (5 min, plus 5 minutes discussion each)

IAB, Director, Co-director, Chairman of the SciLifeLab Board, Infrastructure director, Management Group

11:20 Genomics analysis reveals major determinants of cis-regulatory variation in

Capsella grandiflora - Tanja Slotte 11:30 Age prediction from the plasma proteome - Stefan Enroth

11:40 Loss of chromosome Y (LOY) in blood - a biomarker for cancer and Alzheimer’s disease in aging men - Lars Forsberg

11:50 DNA sequencers in our pockets - Malte Kühnemund 12:00 Spatially resolved transcriptomics visualised in tissue sections - Fredrik Salmén 12:10 The origin of complex cells - Anja Spang

12:20 Working lunch and final closed discussion about management, career development and key challenges

IAB, Director, Co-director, Chair of the SciLifeLab Board, Infrastructure Director 13:30 Discussion and closed session for writing up the report IAB 15:30 Initial feedback to Chairman of the Board IAB, Chairman of the Board, Director; Co-Director 16:00 Return to Stockholm or transfer to Arlanda Airport

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Appendix 2 List of Participants during the IAB meeting

ParticipantsduringIABmeetingMarch8-92017

Name Affiliation RoleatthemeetingInternationalAdvisoryBoardAndersson Bertil NanyangTechnologicalUniversity ChairofIABBrunak Søren TechnicalUniversityofDenmark IABmemberEllenberg Jan EMBLHeidelberg IABmemberHayashizaki Yoshihide RIKENOmicsScienceCentre IABmemberJalkanen Sirpa UniversityofTurku IABmemberJansson Janet PacificNorthwestNationalLaboratory IABmemberKnowles Jonathan UniversityofBasel IABmemberPääbo Svante MPIEvolutionaryAnthropology IABmemberThornton Janet EMBL-EBI IABmemberMayer Tony NanyangTechnologicalUniversity IABsecretarySciLifeLabBoardmembersHeldin Carl-Henrik UppsalaUniversity ChairmanoftheBoardKarlhede Anders StockholmUniversity SciLifeLabBoardSciLifeLabManagementGroupKallioniemi Olli KarolinskaInstitutet DirectorClaesson-Welsh Lena UppsalaUniversity Co-DirectorJenmalm-Jensen Annika KarolinskaInstitutet InfrastructureDirectorGyllensten Ulf UppsalaUniversity ScientificDirectorNilsson Mats StockholmUniversity ScientificDirectorNilsson Peter KTH ScientificDirectorSciLifeLabIntegrationDirectorsEngstrand Ylva StockholmUniversity IntegrationDirectorGustafsson Anders KarolinskaInstitutet viceStefanEriksson(ID)Larhed Mats UppsalaUniversity IntegrationDirectorUhlén Mathias KTH IntegrationDirectorOperationsOfficeSterky Fredrik SciLifeLab HeadofOperationsMolin Eva SciLifeLab ViceHeadofOperationsHammarström Lars SciLifeLab StrategicRelationsOfficer

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RectorsDahlmanWright Karin KarolinskaInstitutet ActingVice-ChancellorofKIKarlsson Sigbritt KTH PresidentofKTHSöderberghWidding Astrid StockholmUniversity Vice-ChancellorofSUÅkesson Eva UppsalaUniversity Vice-ChancellorofUUMinistryofEducationandResearchSchmekel Karin DeputyDirector,MinistryofEducationandResearchPlatformandFacilitypresentationsArvidsson Per SciLifeLab PlatformDirectorBrismar Hjalmar SciLifeLab PlatformDirectorEngström Per SciLifeLab HeadofFacilityGustavsson Anna-Lena SciLifeLab PlatformDirectorGötherström Anders SciLifeLab FacilityDirectorLedin Johan SciLifeLab FacilityDirectorLinnarsson Sten SciLifeLab PlatformDirectorLundeberg Joakim SciLifeLab PlatformDirectorNielsen Jens SciLifeLab HeadofFacilityPersson Bengt SciLifeLab PlatformDirectorRosenquist-Brandell Richard SciLifeLab PlatformDirectorRung Johan SciLifeLab HeadofDataOfficeSchmierer Bernhard SciLifeLab FacilityDirectorSmith Kevin SciLifeLab FacilityDirectorSpjuth Ola SciLifeLab HeadofFacilitySvensson Thomas SciLifeLab FacilityDirectorWirta Valtteri SciLifeLab HeadofFacilityZubarev Roman SciLifeLab FacilityDirectorSciLifeLabFellowsAmunts Alexey SciLifeLab,StockholmUniversity FellowsBienko Magda SciLifeLab,KI FellowsBurki Fabien SciLifeLab,UppsalaUniversity FellowsCarlsson Jens SciLifeLab,UppsalaUniversity FellowsDeindl Sebastian SciLifeLab,UppsalaUniversity FellowsDelemotte Lucie SciLifeLab,KTH FellowsElsässer Simon SciLifeLab,KI FellowsFriedländer Marc SciLifeLab,StockholmUniversity FellowsGlobisch Daniel SciLifeLab,UppsalaUniversity FellowsHudson Paul SciLifeLab,KTH FellowsJonas Kristina SciLifeLab,StockholmUniversity FellowsKutter Claudia SciLifeLab,KI FellowsMardinoglu Adil SciLifeLab,KTH Fellows

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Pelechano Vicente SciLifeLab,KI FellowsPeura Sari SciLifeLab,Chalmers FellowsSellin Mikael SciLifeLab,UppsalaUniversity FellowsSlotte Tanja SciLifeLab,StockholmUniversity FellowsTesta Ilaria SciLifeLab,KTH FellowsHighlightpresentersEnroth Stefan UppsalaUniversity HighlightpresenterForsberg Lars UppsalaUniversity HighlightpresenterKühnemund Malte StockholmUniversity HighlightpresenterLinnarsson Sten KarolinskaInstitutet HighlightpresenterLundeberg Joakim KTH HighlightpresenterRosenquist-Brandell Richard UppsalaUniversity HighlightpresenterSalmén Fredrik KTH HighlightpresenterSlotte Tanja StockholmUniversity HighlightpresenterSpang Anja UppsalaUniversity HighlightpresenterWarpman-Berglund Ulrika KarolinskaInstitutet Highlightpresenter

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Appendix 3 International Advisory Board (IAB) Membership Membership: Chair: Professor Bertil Andersson President, Nanyang Technological University (NTU), Singapore Previously Chief Executive of the European Science Foundation, Rector of Linköping University and Chairman of the Nobel Committee for Chemistry and a Trustee of the Nobel Foundation. Professor Bertil Andersson is a plant biochemist of international reputation. Formerly he was a Professor of Biochemistry and then Dean of Chemical Sciences at Stockholm University. Professor Søren Brunak Professor of Bioinformatics and Director, Disease Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark (TUD) Professor Brunak has pioneered new computational strategies for the analysis of biological data in molecular biology, medicine and biotechnology, especially through machine learning techniques and data integration Dr Jan Ellenberg Interdisciplinary Group Leader, Gene Expression and Cell Biology/Biophysics Programmes and Coordinator, Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany Dr Ellenberg’s fields of interest are in cell biology, especially cell division (mytosis), cell nuclear structures and lice cell imaging. Professor Yoshihide Hayashizaki Advisor to President, Director of Preventive Medical Innovation Programme, RIKEN, Japan He is the pioneer of -omics science and launched the international FANTOM consortium which is the most long-running consortium in the World with over 500 researchers from 20 different nations, as a jamboree-type consortium. He and his FANTOM consortium have analysed transcriptome, promotome, enhancerome and transcriptional network of human and other primates. In 2013, he started the RIKEN Preventive Medicine and Diagnosis Innovation Programme (PMI). The mission of

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PMI is to lead the transformation of medical care to a new era enhanced with -omics and other breakthrough technologies developed in RIKEN. Professor Sirpa Tuulikki Jalkanen Professor of Immunology, Institute of Biomedicine, Turku University, Finland Professor Jalkanen’s research specialisation is in the fields of biomedical and clinical medicine and is one of the world’s leading researchers in the area of lymphocyte migration in the human immune defence system particularly in the treatment of autoimmune diseases and in preventing the spread of cancer. Dr Janet Jansson Division Director of Biological Sciences, Pacific Northwest National Laboratory (PNNL), Richland, Washington State, USA Dr Jansson’s key interest is in microbial ecology and specifically in the use of molecular approaches in the study of complex microbial communities especially those in soil, sediment and the human gut. She is currently coordinating Microbiomes in Transition, a major new PNNL initiative. In her earlier career Dr Jansson had been a member of Stockholm University and the Swedish University of Agricultural Sciences, Uppsala. Professor Jonathan Knowles Distinguished Professor in Personalised Health Care, University of Helsinki, Finland. Visiting Professor, University of Oxford; Visiting Fellow, Pembroke College, Cambridge; Professor Emeritus of Translational Medicine, Ecole Polytechnique Fédérale de Lausanne, Switzerland; Executive Chairman of Immunocore Ltd; and Chairman of Adaptimmune Ltd Professor Knowles’ diverse career experience spans both academia and industry as he served as the president of group research at Hoffmann –La Roche for 12 years, a long term board member of Genentech, Chugai Pharmaceuticals and Caris Life Sciences, and the founding chairman of the Innovative Medicines Initiative.. His research current interests are focused on translational and personalised medicine. Dr Svante Pääbo Director, Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany Dr Pääbo is one of the founders of palaeogenetics focussing on genetics in the study of early humans and other ancient populations. He has published the sequence of the Neanderthal genome and has also identified, through DNA analysis, the Denisovan hominin. Dr Pääbo is an alumnus of Uppsala University where he completed his Ph.D. Dr Dame Janet Thornton, FRS

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Former Director of the European Bioinformatics Institute (EBI) of EMBL, Cambridge, UK Dr Thornton is a leading research in structural bioinformatics. She has worked in molecular biophysics and in biomolecular structures. She coordinated the preparatory phase of the European Life Sciences data infrastructure – ELIXIR. Apologies for Absence: Professor Aviv Regev Director, Klarman Cell Observatory, Broad Institute and Investigator, Howard Hughes Medical Institute and Professor, Department of Biology, MIT, USA Professor Regev’s research focuses on how complex molecular networks function and evolve in the face of genetic and environmental changes. Previously, at Harvard University, Professor Regev has also worked in the biotechnology industry directing bioinformatics research. Tony Mayer IAB Secretary

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Appendix 4 Members of the SciLifeLab Governing Board Chair Carl-Henrik Heldin Uppsala University Industry Representative Margareta Olsson Birgersson Roche Host Universities Representatives Sophia Hober KTH Anders Gustafsson KI Anders Karlhede Stockholm University Stellan Sandler Uppsala University External university Representatives Gunilla Westergren – Thorsson Linköping University Staffan Edén Gothenburg University Marianne Sommarin Umeå University

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Appendix 5 Summary of Recommendations from the IAB Report 2015 1. The SAB is impressed with the initiative to create the SciLifeLab and commends

the Swedish authorities, a number of key individuals and the four hosting universities for their far-sighted actions.

2. Very substantial progress has been made in establishing the SciLifeLab and its

platforms, especially given that it only became operational in mid-2013. 3. Governance and financing reflect the ad-hoc growth of the ScilifeLab. It is now

opportune to revise and streamline both and move to a more efficient operation under the Governing Board, with top level representation from the host universities.

4. There should be budget integration under the Board. 5. SciLifeLab would benefit from a revised or new Mission and Vision statements to

reflect the SciLifeLab’s strategy and ambition, especially in relation to research and the new trends in life sciences to move towards major collaborative programmes. Multidisciplinary Programs with more ambitious goals and social impact would help in increase further the impact of the SciLifeLab both in basic and applied science

6. Future developments spearheaded by the identification and initiation of

collaborative flagships projects across the span of the life sciences community. The Human Protein Atlas is a good example already in existence.

7. The SciLifeLab should give emphasis to the environmental life sciences by

ensuring that environmental research is accorded a full and high priority within the work programmes.

8. Procedures for accessing the technological platforms need to be revised based

on a peer-review system for both quality control and transparency.

9. We strongly endorse the evaluation of the technological platforms in the first half of 2016 in which some members of the IAB are willing to participate.

10. The regional facilities, as defined today, are not an integral part of the SciLifeLab

and we advocate a 2-tier structure with a core and satellites, open for enlargement as life sciences research develops. The regional platforms are the responsibility (including funding) of the host institutions unless they can demonstrate a national relevance (after peer review) in which case they would become constituent platforms within SciLifeLab.

11. Attention needs to be given to career development and professional training of

the service staff of the technological platforms and their constituent facilities.

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12. There is a need for leadership and better coordination in creating further industrial

and societal collaborations and providing procedures and best practice for them.

13. Ideally there should be a single unit for innovation exploitation or at least a very strong coordination between the four universities in this area.

14. There is a need for dedicated mentorship of younger faculty to develop their

academic progress and innovation capacity, and especially for those recruited from abroad to ease their way into the Swedish academic and funding system.

15. There is a requirement for the dedicated engagement of senior faculty from the

parent universities in SciLifeLab coupled with their relocation to and physical presence in the SciLifeLab.

16. Even more pro-active efforts are needed to integrate the two geographically

separate nodes. 17. SciLifeLab facilities should be optimised to create the physical exchange between

those involved in the SciLifeLab. Common activities and space are needed and the Stockholm node, in particular, suffers from a lack of informal common meeting spaces.

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Appendix 6 ExplanationofOrganisationDiagram–Figure1(NotebytheDirector)The "blue people” in the Figure, meaning the Director, Co-Director and Infrastructure Director represent the national board and, therefore, their mandate is towards the national funding. In addition, they have roles towards coordinating the rest of the organization (although in the latter they may not have a clear mandate here). Thus, even though each was hired by one of the host Universities (Director and Infrastructure Director by KI, Co-Director by UU) their primary, if not exclusive, mission is towards the national board and SciLifeLab as a whole (not a specific university). The "red people" in the Figure, i.e. the Scientific Directors at SciLifeLab, are each the representatives of the host universities in the management group. Their mandate is both towards the host university as well as towards the national board. They participate every other week in the management group activities and are, therefore, “hands-on” and represent people who know SciLifeLab well. They represent the SciLifeLab associated staff from each university at the management group and also mediate issues from inside SciLifeLab towards each university. The Scientific Directors participate in the meetings of the SciLifeLab committees of each University, even though they may not have executive power. The Integration Directors are all part of the SciLifeLab committees of the host universities. Most of them work in fairly high leadership positions at the host universities (e.g. Deans and Infrastructure Vice-Rectors) and sometimes act as the chair of the SciLifeLab committee for that University. Twice per semester, they will come to a joint meeting with the management group at SciLifeLab. They take care of the integration of SFO and national funding at each university. The dual roles of Scientific Directors and Integration Directors was arranged this way as in the discussions with the Rectors, it was impossible to find a single person who could be both hands-on at SciLifeLab and have time to represent the University and at the same time possess executive responsibility towards the Rector at each host University. Thus, a two-person model was the compromise

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Appendix 7 Site Management of the SciLifeLab in Solna (Note by the Director) The whole building complex consist of three major parts (Alfa, Beta and Gamma) and Delta that connects the three (including the lobby). Akademiska Hus, which is one of Sweden’s biggest real-estate companies owns the buildings (like much of academic and research building across the country). SciLifeLab rents Alfa (100%) and Gamma (80%). 20% of Gamma is rented by different KI units related to commercialisation activities, while Beta is for the private company - Sobi. In practice, it is more complicated in that KTH rents the SciLifeLab space from KI which has the first-hand contract with Akademiska Hus. As the primary host for SciLifeLab, KTH manages the cost distribution to the end users at each of the three universities (KTH, KI and SU). The three universities in Stockholm (KI, KTH and SU) will manage space allocation in the buildings through the newly set up "Campus Solna Committee”. Previously, the so-called Stockholm steering group (2010-2016) handled space allocations. However, in the new organization structure started in 2017, the members in the Campus Solna committee are the Scientific Directors (KI, KTH and SU), the Integration Directors (KI, KTH and SU) and the SciLifeLab Infrastructure Director. The platforms and facilities will have priority for space. The Campus Solna committee will manage the rules for space reallocations that will be needed now that the Alpha-Gamma spaces are 99% occupied or at least 99% reserved. Therefore, the Director is not in direct control of the space but can influence decisions via the members of the new management group.