Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Where is the Market? Evidence from Cross-Listings in the U.S.

We explore two main questions. First, can two markets for a company’s shares coexist and, if so, what determines the distribution of trading volume across them? For firms cross-listed in the U.S. we find that in most cases U.S. trading is a significant fraction of total volume, and tends to be larger for companies based in countries that are geographically close, with low financial development and poor anti-insider trading protection. Moreover, the relative size of the U.S. market is larger if the company is small, volatile and high-tech. Second, we ask whether developing an active foreign market entails lower domestic trading activity. We find that for firms based in developed markets, the domestic turnover rate increases in the wake of cross-listing and remains permanently higher. In contrast, emerging market firms tend to experience a decrease in domestic trading activity.trading volume, cross-listing, flow-back

Evaluation of Lolium perenne L. cv. AberDart and AberDove for silage production

peer-reviewedThe objective of this study was to assess the value, for silage production, of intermediateheading Lolium perenne L. cultivars, AberDart and AberDove (diploid), bred for increased water-soluble carbohydrate (WSC) concentrations, relative to four control cultivars (Fennema, AberElan and Spelga (diploid), and Greengold (tetraploid)). Cultivars were evaluated for forage dry matter (DM) yield, ground cover and indirect laboratory measures of nutritional value and ensilability over 3 harvest years within intensive silage-production systems. AberDove was the most desirable diploid for silage production producing on average 316 kg/ha higher (2%) DM yield per annum, having a 10 g/kg higher (1%) dry matter digestibility (DMD) and, based primarily on a 6 g/L higher (19%) concentration of WSC expressed in the aqueous extract (WSCAE), offered the greatest potential to produce well preserved silage. Ensiling AberDart compared to the diploid controls offered a slightly greater probability of producing well preserved silage based on a modest increase of 2 g/L (6%) in WSCAE concentration. The dilemma for silage production is that AberDart, on average produced 558 kg/ha less (4%) DM yield per annum but had a greater (1%) DMD of 6 g/kg than the diploid controls. The tetraploid control had, on average, 13 and 8 g/kg higher (2% and 1%, respectively) DMD than AberDart and AberDove, but at a cost of lower ensilability with lower (6% and 21%, respectively) WSCAE values of 2 and 6 g/L. In its favour, the tetraploid control outyielded AberDart by, on average, 917 kg/ha DM per annum (7%) and produced comparable yields to AberDove. Final ground cover ratings were high (≥ 95%) for all cultivars. Evaluation of nutritional value and ensilability offers further grounds to differentiate and select cultivars for animal production potential.A Teagasc Walsh Fellowship, awarded to P. Conaghan and H. Howard, and the European Commission under the Fifth Framework Programme (QLK5-CT-2001-0498) supported this research

Uthållighet och avkastning hos sorter av engelskt rajgräs, rajsvingel och rörsvingel

Målsättningen med projektet var att testa uthålligheten hos sorter av engelskt rajgräs,rajsvingel och rörsvingelhybrid under fältförhållande i södra och mellersta Sverige för att kunna ge rekommendationer till lantbrukarna. Ordinarie sortförsöken förlängdes under perioden 2009-2011 med ett tredjeoch fjärde vallår. Totalt nio försök ingick på fyra olika platser. Avkastning, marktäckning och skottvikt bestämdes. Resultaten visar att arterna uppförde sig olika i Götaland jämfört med Svealand. Rajsvingel var betydligt uthålligare i Götaland än i Svealand, men engelskt rajgräs hade lika stor nedgång i avkastning I första skörd i de två områdena. Rörsvingel och rörsvingelhybrid var de två uthålligaste arterna med stabilast avkastning över fyra vallår, med det fanns sortskillnader inom rörsvingelhybriden. Rörsvingelhybriden Hykor hade stor variation i uthållighet i Svealand. Marktäckning och mängden levande skott på våren var ett bra sätt att mäta vinterskadornaoch beståndets tillväxtpotential

Copyright Charges: A Library's Approach to Reducing its Copyright Fees

Medical Sciences Library (MSL) at Texas A&M University offers ILL services to its affiliates free of charge. Like many other libraries, ILL staff first try to borrow from free libraries to keep the borrowing fees as low as possible. However, copyright fees are often higher than the charges of borrowing an article. To offset the copyright charges and maintain the free service, a new plan was devised by the librarian overseeing ILL. After consulting with the director, an acceptable range of copyright fees was chosen for each patron group (undergraduate, graduate, staff, faculty). This breakdown was forwarded to staff and they were asked to follow a series of steps when copyright needs to be paid for a request. This poster will explain the steps in detail and provide the outcome

Updated taxonomy of Lactifluus section Luteoli : L. russulisporus from Australia and L. caliendrifer from Thailand

Lactifluus russulisporus Dierickx & De Crop and Lactifluus caliendrifer Froyen & De Crop are described from eucalypt forests in Queensland, Australia and different forest types in Thailand, respectively. Both species have recently been published on Index Fungorum and fit morphologically and molecularly in L. sect. Luteoli, a section within L. subg. Gymnocarpi that encompasses species with alboochraceous basidiomes, white latex that stains brown and typical capitate elements in the pileipellis and/or marginal cells

Ekologisk sortprovning av vallväxter

Vallgräsen missgynnas ofta i en ekologisk vall genom sämre kväveförsörjning än baljväxterna, och därför är sorternas konkurrensförmåga i blandvall en viktig egenskap att undersöka. Sorter av timotej, ängssvingel, och engelskt rajgräs provas i blandning med baljväxt för att efterlikna praktiska förhållanden. Fem handelssorter per art har valts ut, vilka representerar etablerade och i en nära framtid, ny sorter på marknaden. Försök har anlagts på tre platser för att spegla olika förhållanden i södra och mellersta Sverige. Eftersom förhållandet mellan gräs och baljväxt förändras över tiden är det viktigt att studera uthålligheten i minst tre skördeår. Målet är att under ekologisk provning bestämma skillnad i avkastning, konkurrensförmåga och näringsinnehåll mellan sorter av timotej, ängssvingel, och engelskt rajgräs. Projektet finansieras 2003-2008 av Jordbruksverket

Investigation of base-isolated structures during recent earthquakes and computer simulations utilizing near-source long-period ground motions

The current study contains two major parts. Part One consists of the identification and analysis of three existing base-isolated buildings in Southern California. The identification and analysis utilize the recorded motions of these structures from past earthquakes. System identification is useful for understanding the extent to which the structures enter the nonlinear realm and how much their properties change. Models are constructed assuming completely elastic three-dimensional superstructures, with idealized bi-linear hysteretic elements for the isolating bearings. The properties used in the bearing models were taken from tests of the actual bearings before installation. The models were then verified by comparing their responses computed using the various recorded foundation ground motions, with the recorded responses of the actual structures. The models were adjusted to minimize the error of several response quantities. Part Two contains computer simulations subjecting a typical base-isolated building (TBIB) to two classes of ground motions. The first is a sampling of near-source recorded motion from past moderate-to-large earthquakes. The second is a group of synthetic near-source motions generated for a hypothetical M 7.0 earthquake. In some cases, the lateral response of the model exceeds the isolation gap, indicating that the displacement barrier would be impacted. In order to further study base-isolated buildings when the isolation bearings undergo large displacements the (TBIB) model is used and the computer program 2D-BUMP is developed. This program includes the effects of a fully nonlinear superstructure, nonlinear springs acting as displacement barriers which engage at specified distances, and a tri-linear model for the elastomeric bearings. Using this model, several conclusions are drawn regarding the probable areal extent of damaging near-source ground motions from the M 7.0 event, as well as the behavior of base-isolated structures due to these near-source long-period ground motions