Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005-1013. (c) 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Synthesis of Instruction Extensions on HyperCell, a Reconfigurable Datapath

In this paper we present HyperCell as a reconfigurable datapath for Instruction Extensions (IEs). HyperCell comprises an array of compute units laid over a switch network. We present an IE synthesis methodology that enables post-silicon realization of IE datapaths on HyperCell. The synthesis methodology optimally exploits hardware resources in HyperCell to enable software pipelined execution of IEs. Exploitation of temporal reuse of data in HyperCell results in significant reduction of input/output bandwidth requirements of HyperCell.

A Dynamic Loading Device for Suction Foundations in Centrifuge Modeling

Suction bucket foundations are widely used in the offshore platform for the exploitation of the offshore petroleum and natural gas resources. During winter seasons, ice sheets formed in Bohai Bay will impose strong impact and result in strong vibration on the platform. This paper describes a dynamic loading device developed on the geotechnical centrifuge and its application in modeling suction bucket foundation under the equivalent ice-induced vibration loadings. Some experimental results are presented. It is shown that when the loading amplitude is over a critical value, the sand at the upper part around the bucket softens or even liquefies. The excess pore pressure decreases from the upper part to the lower part of the sand foundation in vertical direction while decreases from near to far away from the bucket's side wall in the horizontal direction. Large settlements of the bucket and the sand around the bucket occur under the horizontal dynamic loading. The dynamic responses of the bucket with smaller size are heavier.

R&D Policy in Economies with Endogenous Growth and Non-Renewable Resources

The aim of this paper is to analyze how active R&D policies affect the growth rate of an economy with endogenous growth and non-renewable resources. We know from Scholz and Ziemens (1999) and Groth (2006) that in infinitely lived agents (ILA) economies, any active R&D policy increases the growth rate of the economy. To see if this result also appears in economies with finite lifetime agents, we developed an endogenous growth overlapping generations (OLG) economy à la Diamond which uses non-renewable resources as essential inputs in final good’s production. We show analytically that any R&D policy that reduces the use of natural resources implies a raise in the growth rate of the economy. Numerically we show that in economies with low intertemporal elasticity of substitution (IES), active R&D policies lead the economy to increase the depletion of non-renewable resources. Nevertheless, we find that active R&D policies always imply increases in the endogenous growth rate, in both scenarios. Furthermore, when the IES coefficient is lower (greater) than one, active R&D policies affect the growth rate of the economy in the ILA more (less) than in OLG economies.

Second-best tax policy in a growing economy with externalities

This paper investigates the exploitation of environmental resources in a growing economy within a second-best scal policy framework. Agents derive utility from two types of consumption goods one which relies on an environmental input and one which does not as well as from leisure and from environmental amenity values. Property rights for the environmental resource are potentially incomplete. We connect second best policy to essential components of utility by considering the elasticity of substitution among each of the four utility arguments. The results illustrate potentially important relationships between environmental amentity values and leisure. When amenity values are complementary with leisure, for instance when environmental amenities are used for recreation, taxes on extractive goods generally increase over time. On the other hand, optimal taxes on extractive goods generally decrease over time when leisure and environmental amenity values are substitutes. Unders some parameterizations, complex dynamics leading to nonmonotonic time paths for the state variables can emerge.

Growth in Overlapping Generation Economies with Non-Renewable Resources

Published as an article in: Journal of Environmental Economics and Management, 2005, vol. 50, issue 2, pages 387-407.

Web resources to disseminate methodology in heritage documentation

Impreso por la Diputación Foral de Álava, D.L. VI-430/99.

Your water resources

(26 page document)