From perfect strangers to research partners: a study of relationships, resource sharing and perceived benefits within R&D cooperation networks

Doctoral thesis in Marketing and Strategy.

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.

BACKGROUND: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. RESULTS: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. CONCLUSION: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

Resource management research in Passive Optical Networks (PON)

Next Generation Access Networks (NGAN) are the new step forward to deliver broadband services and to facilitate the integration of different technologies. It is plausible to assume that, from a technological standpoint, the Future Internet will be composed of long-range high-speed optical networks; a number of wireless networks at the edge; and, in between, several access technologies, among which, the Passive Optical Networks (xPON) are very likely to succeed, due to their simplicity, low-cost, and increased bandwidth. Among the different PON technologies, the Ethernet-PON (EPON) is the most promising alternative to satisfy operator and user needs, due to its cost, flexibility and interoperability with other technologies. One of the most interesting challenges in such technologies relates to the scheduling and allocation of resources in the upstream (shared) channel. The aim of this research project is to study and evaluate current contributions and propose new efficient solutions to address the resource allocation issues in Next Generation EPON (NG-EPON). Key issues in this context are future end-user needs, integrated quality of service (QoS) support and optimized service provisioning for real time and elastic flows. This project will unveil research opportunities, issue recommendations and propose novel mechanisms associated with the convergence within heterogeneous access networks and will thus serve as a basis for long-term research projects in this direction. The project has served as a platform for the generation of new concepts and solutions that were published in national and international conferences, scientific journals and also in book chapter. We expect some more research publications in addition to the ones mentioned to be generated in a few months.

Kinship in entrepreneur networks: Performance effects of resource assembly in Africa

We examine the relationship between structural social capital, resource assembly, and firm performance of entrepreneurs in Africa. We posit that social capital primarily composed of kinship or family ties helps the entrepreneur to raise resources, but it does so at a cost. Using data drawn from small firms in Kampala, Uganda, we explore how shared identity among the entrepreneur's social network moderates this relationship. A large network contributed a higher quantity of resources raised, but at a higher cost when shared identity was high. We discuss the implications of these findings for the role of family ties and social capital in resource assembly, with an emphasis on developing economies.

Improving Transition Outcomes: Resource Mapping Workshop: Resource List

Resource Mapping resources shared during the Improving Transition Outcomes Resource Mapping Workshops

Improving Transition Outcomes: Resource Mapping Workshop: General Information

Information shared at the Improving Transition Outcomes Resource Mapping Workshops

Improving Transition Outcomes: Resource Mapping Workshop: Interview Tips

Interview tips developed by Lois Smidt with Beyond Welfare in Ames, Iowa and shared at the Improving Transition Outcomes Resource Mapping Workshops

Improving Transition Outcomes: Resource Mapping Workshop: What is Resource Mapping?

Information shared at the Improving Transition Outcomes Resource Mapping Workshops

ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

Project Resource Management in R&D Public Sector Organization

In R&D organizations multiple projects are executed concurrently. Problems arises in managing shared resources since they are needed by multiple projects simultaneously. The objective of this thesis was to study how the project and resource management could be developed in a public sector R&D organization. The qualitative research was carried out in the Magnetic Measurements section at CERN where the section measures magnets for particle accelerators and builds state of the art measurement devices for various needs. Hence, the R&D and measurement projects are very time consuming and very complex. Based on the previous research and the requirements from the organization the best alter- native for resource management was to build a project management information system. A centralized database was constructed and on top of it was built an application for interacting and visualizing the project data. The application allows handling project data, which works as a basis for resource planning before and during the projects are executed. It is one way to standardize the work-flow of projects, which strengthens the project process. Additionally, it was noted that the inner customer’s database, the measurement system and the new application needed to be integrated. Further integration ensures that the project data is received efficiently from customers and available not only within the application but also during the concrete work. The research results introduced a new integrated application, which centralizes the project information flow with better visibility.

Connected to Shared Drive Video demo

Staff only video on connecting to WSA Shared from a Mac. ***Note you must be on a secure connection - this means either a wired (ethernet) cable at work or connected to VPN for VPN support call Serviceline.

Resource allocation analysis of the stochastic diffusion search

The Stochastic Diffusion Search (SDS) was developed as a solution to the best-fit search problem. Thus, as a special case it is capable of solving the transform invariant pattern recognition problem. SDS is efficient and, although inherently probabilistic, produces very reliable solutions in widely ranging search conditions. However, to date a systematic formal investigation of its properties has not been carried out. This thesis addresses this problem. The thesis reports results pertaining to the global convergence of SDS as well as characterising its time complexity. However, the main emphasis of the work, reports on the resource allocation aspect of the Stochastic Diffusion Search operations. The thesis introduces a novel model of the algorithm, generalising an Ehrenfest Urn Model from statistical physics. This approach makes it possible to obtain a thorough characterisation of the response of the algorithm in terms of the parameters describing the search conditions in case of a unique best-fit pattern in the search space. This model is further generalised in order to account for different search conditions: two solutions in the search space and search for a unique solution in a noisy search space. Also an approximate solution in the case of two alternative solutions is proposed and compared with predictions of the extended Ehrenfest Urn model. The analysis performed enabled a quantitative characterisation of the Stochastic Diffusion Search in terms of exploration and exploitation of the search space. It appeared that SDS is biased towards the latter mode of operation. This novel perspective on the Stochastic Diffusion Search lead to an investigation of extensions of the standard SDS, which would strike a different balance between these two modes of search space processing. Thus, two novel algorithms were derived from the standard Stochastic Diffusion Search, ‘context-free’ and ‘context-sensitive’ SDS, and their properties were analysed with respect to resource allocation. It appeared that they shared some of the desired features of their predecessor but also possessed some properties not present in the classic SDS. The theory developed in the thesis was illustrated throughout with carefully chosen simulations of a best-fit search for a string pattern, a simple but representative domain, enabling careful control of search conditions.

The shared influence of phylogeny and ecology on the reproductive patterns of Myrteae (Myrtaceae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Survivable Lightpath Provisioning in WDM Mesh Networks Under Shared Path Protection and Signal Quality Constraints

This paper addresses the problem of survivable lightpath provisioning in wavelength-division-multiplexing (WDM) mesh networks, taking into consideration optical-layer protection and some realistic optical signal quality constraints. The investigated networks use sparsely placed optical–electrical–optical (O/E/O) modules for regeneration and wavelength conversion. Given a fixed network topology with a number of sparsely placed O/E/O modules and a set of connection requests, a pair of link-disjoint lightpaths is established for each connection. Due to physical impairments and wavelength continuity, both the working and protection lightpaths need to be regenerated at some intermediate nodes to overcome signal quality degradation and wavelength contention. In the present paper, resource-efficient provisioning solutions are achieved with the objective of maximizing resource sharing. The authors propose a resource-sharing scheme that supports three kinds of resource-sharing scenarios, including a conventional wavelength-link sharing scenario, which shares wavelength links between protection lightpaths, and two new scenarios, which share O/E/O modules between protection lightpaths and between working and protection lightpaths. An integer linear programming (ILP)-based solution approach is used to find optimal solutions. The authors also propose a local optimization heuristic approach and a tabu search heuristic approach to solve this problem for real-world, large mesh networks. Numerical results show that our solution approaches work well under a variety of network settings and achieves a high level of resource-sharing rates (over 60% for O/E/O modules and over 30% for wavelength links), which translate into great savings in network costs.

A Load-Balancing Shared-Protection-Path Reconfiguration Approach in WDM Wavelength-Routed Networks

Wavelength-routed networks (WRN) are very promising candidates for next-generation Internet and telecommunication backbones. In such a network, optical-layer protection is of paramount importance due to the risk of losing large amounts of data under a failure. To protect the network against this risk, service providers usually provide a pair of risk-independent working and protection paths for each optical connection. However, the investment made for the optical-layer protection increases network cost. To reduce the capital expenditure, service providers need to efficiently utilize their network resources. Among all the existing approaches, shared-path protection has proven to be practical and cost-efficient [1]. In shared-path protection, several protection paths can share a wavelength on a fiber link if their working paths are risk-independent. In real-world networks, provisioning is usually implemented without the knowledge of future network resource utilization status. As the network changes with the addition and deletion of connections, the network utilization will become sub-optimal. Reconfiguration, which is referred to as the method of re-provisioning the existing connections, is an attractive solution to fill in the gap between the current network utilization and its optimal value [2]. In this paper, we propose a new shared-protection-path reconfiguration approach. Unlike some of previous reconfiguration approaches that alter the working paths, our approach only changes protection paths, and hence does not interfere with the ongoing services on the working paths, and is therefore risk-free. Previous studies have verified the benefits arising from the reconfiguration of existing connections [2] [3] [4]. Most of them are aimed at minimizing the total used wavelength-links or ports. However, this objective does not directly relate to cost saving because minimizing the total network resource consumption does not necessarily maximize the capability of accommodating future connections. As a result, service providers may still need to pay for early network upgrades. Alternatively, our proposed shared-protection-path reconfiguration approach is based on a load-balancing objective, which minimizes the network load distribution vector (LDV, see Section 2). This new objective is designed to postpone network upgrades, thus bringing extra cost savings to service providers. In other words, by using the new objective, service providers can establish as many connections as possible before network upgrades, resulting in increased revenue. We develop a heuristic load-balancing (LB) reconfiguration approach based on this new objective and compare its performance with an approach previously introduced in [2] and [4], whose objective is minimizing the total network resource consumption.