Work
Package 03

This task will prepare agreements and sign protocols allowing the access and use of infrastructures and equipment that are already available, thus concentrating funds on the recruitment of human resources and other activities essential to the implementation of the CoE. To this end, a protocol will be signed with UP, allowing the establishment of BIOPOLIS at Campus de Vairão, which is owned by the University. These facilities are already used by ICETA-CIBIO, but the areas available and the terms of use will be upgraded following the signature of the new agreement. Overall, the facilities already available are sufficient to accommodate the BIOPOLIS staff, and to give office and lab conditions to researchers, with only limited upgrading required as described in T3.4. The transition of lab and field equipment used by CIBIO from ICETA to BIOPOLIS CoE will be defined in the protocol described in T1.2, detailing the conditions upon which the physical resources will be used. In addition, protocols will be signed with external entities to provide access to other facilities that are important to fulfill the Vision and Mission of BIOPOLIS, namely to establish field stations in other regions of Portugal (e.g., Estação Biológica de Mértola) and TwinLabs (T4.3) in African countries. Protocols will be reviewed whenever necessary.

The objective of this task is to prepare guidelines, and to implement and monitor the management of infrastructures and equipment of the CoE. The first step will be the creation of an Infrastructures and Equipment Committee; which will be designated by the BoD and will include 2 technicians and 3 researchers. The Committee may be expanded and its composition changed if needed to accomplish its tasks. The Committee will work together with the Technical Support Unit to prepare a Management Plan of Infrastructures (including IT) and Equipment, which shall include an inventory of the physical resources available initially, identifying their current condition and maintenance needs, and setting the principles whereby they will be accessed by researchers and technicians. A booking and prioritisation system will be established to define access to lab and field facilities and equipment. The Committee will also work with IT Officers for developing an online database and management system of infrastructures and equipment, including critical information on their use and users, scheduled maintenance, depreciation rates, and so on. Once approved, the Management Plan of Infrastructures (including IT) and Equipment will be implemented and monitored by technical staff, in close collaboration with the Committee. A revision of the Plan will be made on year 4, or earlier if needed due to significant upgrade of BIOPOLIS physical resources (T3.3).

The management of IT infrastructure will be given particular importance in the development of BIOPOLIS activities. This is critical not only for the daily activities of the CoE, but also for processing the vast volumes of data generated for instance by NGS, bio-loggers and remote sensing. BIOPOLIS CoE will set up an IT Committee to deal with all the aspects of the computational infrastructure, which will include the IT Officer(s) and senior researchers with expertise in bioinformatics and computational biology. One of the missions of the Committee will be to link BIOPOLIS with other high-level computational infrastructures, including the FCT’s FCCN infrastructure, the Advanced Supercomputing Centre at the University of Minho, and the European Grid Infrastructure (EGI). The Committee will set guidelines of access to the IT infrastructure, will propose a plan for its maintenance and progressive upgrading, and will guarantee its functioning to assure the daily requirements of the CoE. The UM will share with BIOPOLIS CoE staff its long experience of management and use of IT infrastructure and, in the frame of projects developed jointly, the UM resources will be made available to BIOPOLIS members.

The Infrastructures and Equipment Committee will prepare a Plan of Infrastructure Upgrade and Re-Equipment, to be implemented over time with funding other than through Teaming. This Plan will cover mainly the infrastructures and equipment available at BIOPOLIS headquarters in Campus de Vairão, but may consider other facilities needed for BIOPOLIS activity, including field stations (e.g., Estação Biológica de Mértola) and TwinLabs (T4.3). This is essential to guarantee that the infrastructures and equipment available to BIOPOLIS match its considerable ambition of developing excellent research towards innovation, thus allowing the CoE to grow progressively and to acquire state-of the-art equipment. The equipment plan will be established in close collaboration with UM, considering the numerous platforms that already exist at this partner. Indeed, UM is running in a structured manner a network of platforms in Biological Sciences and will provide advice. Specific effort will be made to ensure complementarity of the equipment and know-how between BIOPOLIS and UM, and cooperation and mutual access to each other’s facilities through joint projects. Priority will be placed on developing in BIOPOLIS the facilities that need to be available in situ to be operational, and on developing partnerships with existing UM platforms that do not enter this category. Based on the Research Programme of BIOPOLIS and the initial equipment that will be available, the re-equipment will focus on various equipment that will be acquired in the short, medium and long term, and that will be assigned to the research and support platforms detailed in Table 1.3a. The exact technical characteristics of the equipment, the calendar of acquisition, the acquisition procedures, and so forth will be defined in the Plan of Infrastructure Upgrade and Re-Equipment. The Plan will be prepared in the 2nd year and revised after 3 years.