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3. V. 1.0.2

Author

Philippe, O., Hammitzsch, M., Janosch, S., van der Walt, A., van Werkhoven, B., Hettrick, S., Katz, D., Leinweber, K., Gesing, S., Druskat, S., Henwood, S., May, N., Lohani, N., and Sinha, M.

Published
2019

4. A Science Gateway for Biodiversity and Climate Change Research

Author

Elia, D., Nuzzo, A., Nassisi, P., Fiore, S., Blanquer, I., Brasileiro, F.V., Rufino, I.A.A., Seijmonsbergen, A.C., Anders, N.S., de O. Galavo, O., de B.L. Cunha, J.E., Sousa-Baena, M., Canhos, V.P., Aloisio, G., Gesing, S., Krüger, J., and Computational Geo-Ecology (IBED, FNWI)

Subjects
GeneralLiterature_MISCELLANEOUS
Abstract

Climate and biodiversity systems are closely interlaced across a wide range of scales. To better understand the mutual interaction between climate change and biodiversity there is a strong need for multidisciplinary skills, tools and a large variety of heterogeneous, distributed data sources. In this regard, the EUBrazilCloudConnect project provides a user-centric research environment built on top of a federated cloud infrastructure across Europe and Brazil to serve scientific needs. One of the test cases implemented in this project focuses on climate change and biodiversity research. The BioClimate is the Science Gateway of the use case. It aims at providing the end-users with a highly integrated environment, addressing mainly data analytics requirements. This paper presents a complete overview about BioClimate and the scientific environment delivered to the user community at the end of the project.

Published
2017

5. Lightning talk: 'I solemnly pledge': A manifesto for personal responsibility in the engineering of academic software

Author

Allen, A., Aragon, C., Becker, C., Carver, J.C., Chis, A., Combemale, B., Croucher, M., Crowston, K., Garijo, D., Gehani, A., Goble, C., Haines, R., Hirschfeld, R., Howison, J., Huff, K., Jay, C., Katz, D.S., Kirchner, C., Kuksenok, K., Lämmel, R., Nierstrasz, O., Turk, M., van Nieuwpoort, R.V., Vaughn, M., Vinju, J., Allen, G., Carver, J., Choi, S.-C.T., Crick, T., Crusoe, M.R., Gesing, S., Heroux, M., Hwang, L.J., Niemeyer, K.E., Parashar, M., Venters, C.C., System and Network Engineering (IVI, FNWI), and Faculty of Science

Abstract

Software is fundamental to academic research work, both as part of the method and as the result of research. In June 2016 25 people gathered at Schloss Dagstuhl for a week-long Perspectives Workshop and began to develop a manifesto which places emphasis on the scholarly value of academic software and on personal responsibility. Twenty pledges cover the recognition of academic software, the academic software process and the intellectual content of academic software. This is still work in progress. Through this lightning talk, we aim to get feedback and hone these further, as well as to inspire the WSSSPE audience to think about actions they can take themselves rather than actions they want others to take. We aim to publish a more fully developed Dagstuhl Manifesto by December 2016.

Published
2016

6. A model for information and action flows connecting science gateways to distributed computing infrastructures

Author

Pierantoni, G., Frost, D., Gesing, S., Olabarriaga, S., Jaghoori, M., Terstyanszky, G., Arshaid, J., Epidemiology and Data Science, and APH - Methodology

Subjects
Information flows, Distributed computing infrastructures, Einfrastructures, Workflow management systems, Interoperability, Escience portals, Science Gateways, Workflows
Abstract

To support scientists of different disciplines, different fields of Computer Science have developed tools and infrastructures with the aim of giving them access to vast computational resources in the easiest possible way. Such extremely complex structures have evolved naturally in the last decades both in depth and breath and, in addition to scientists, a plethora of heterogeneous actors (system administrators, developers, etc.) cooperate and interact with them. This complex and unstructured flow of actions and information poses difficulties in the development and usage of Science Gateways because information can be missing or hard to isolate at the right layer. In this paper, we aim to start a discussion on how to best manage these information flows to help the design and implementation of more flexible and userfriendly Science Gateways and workflow management systems in the future.

Published
2016

7. Lightning talk: Software impact measurement at the Netherlands eScience center

Author

van Hage, W., Maassen, J., van Nieuwpoort, R., Allen, G., Carver, J., Choi, S.-C.T., Crick, T., Crusoe, M.R., Gesing, S., Haines, R., Heroux, M., Hwang, L.J., Katz, D.S., Niemeyer, K.E., Parashar, M., Venters, C.C., ABS Other Research (FEB), and System and Network Engineering (IVI, FNWI)

Abstract

In this lightning talk we present a new initiative at the Netherlands eScience Center (NLeSC) that aims to measure software impact, recognizing software as research output.

Published
2016

9. User-Friendly Workflows in Quantum Chemistry

Author

Herres-Pawlis, S., Hoffmann, A., Gesing, S., Jens Krüger, Balasko, A., Kacsuk, P., Grunzke, R., Birkenheuer, G., Packschies, L., Brinkmann, A., Terstyansky, G., Weingarten, N., and Kiss, T

Subjects
InformationSystems_INFORMATIONSYSTEMSAPPLICATIONS, QA75 Electronic computers. Computer science / számítástechnika, számítógéptudomány
Published
2013

12. HealthGrid Applications and Technologies meet Science Gateways for Life Sciences, proceedings of HealthGrid 2012

Author

Gesing, S., Glatard, T., Krüger, J., Delgado Olabarriaga, S., Solomonides, T., Silverstein, J.C., Montagnat, Johan, Gaignard, A., Krefting, D., Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Images et Modèles, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Amsterdam [Amsterdam] (UvA), CCRI, NorthShore University HealthSystem, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe MODALIS, Scalable and Pervasive softwARe and Knowledge Systems (Laboratoire I3S - SPARKS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Applied Sciences of Berlin, and Technische Universität Berlin (TU)

Subjects
[INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

International audience; The integration of grid, cloud and other e-infrastructures into the fields of biology, bioinformatics, biomedicine, and healthcare are crucial if optimum use is to be made of the latest high-performance and distributed computer technology in these areas. Science gateways are concerned with offering intuitive graphical user interfaces to applications, data, and tools on distributed computing infrastructures. This book presents the joint proceedings of the Tenth HealthGrid Conference and the Fourth International Workshop on Science Gateways for Life Sciences (IWSG-Life), held in Amsterdam, the Netherlands in May 2012. The HealthGrid conference promotes the exchange and debate of ideas, technologies and solutions likely to promote the integration of grids into biomedical research and health in the broadest sense. The IWSG-Life workshop series is a forum that brings together scientists from the field of life sciences, bioinformatics, and computer science to advance computational biology and chemistry in the context of science gateways. These events have been jointly organized to maximize the benefit from synergies and stimulate the forging of further links in joint research areas. HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences is divided into three parts. Part I includes contributions accepted to the HealthGrid conference; Part II contains the papers about various aspects of the development and usage of science gateways for life sciences. The joint session is recorded in Part III, and addresses the topic of science gateways for biomedical research. This book will provide insights and new perspectives for all those involved in the research and use of infrastructures and technology for healthcare and life sciences.

Published
2012

13. Integrated support for neuroscience research: from study design to publication

Author

Shahand, S., Caan, M.W.A., van Kampen, A.H.C., Olabarriaga, S.D., Gesing, S., Glatard, T., Krüger, J., Delgado Olabarriaga, S., Solomonides, T., Silverstein, J.C., Montagnat, J., Gaignard, A., Krefting, D., Biosystems Data Analysis (SILS, FNWI), and Faculteit der Geneeskunde

Abstract

Computational neuroscience is a new field of research in which neurodegenerative diseases are studied with the aid of new imaging techniques and computation facilities. Researchers with different expertise collaborate in these studies. A study requires scalable computational and storage capacity and information management facilities to succeed. Many virtual laboratories are proposed and developed to facilitate these studies, however most of them cover only the parts related to the computational data processing. In this paper we describe and analyse the phases of the computational neuroscience studies including the actors, the tasks they perform, and the characteristics of each phase. Based on these we identify the required properties and functionalities of a virtual laboratory that supports the actors and their tasks throughout the complete study.

Published
2012

15. iBRAIN2: Automated analysis and data handling for RNAi screens

Author

Gesing, Sandra, Glatard, Tristan, Olabarriaga, Silvia Delgado, Solomonides, Tony, Silverstein, Jonathan C, Montagnat, Johan, Gaignard, Alban, Krefting, Dagmar, Gesing, S ( Sandra ), Glatard, T ( Tristan ), Olabarriaga, S D ( Silvia Delgado ), Solomonides, T ( Tony ), Silverstein, J C ( Jonathan C ), Montagnat, J ( Johan ), Gaignard, A ( Alban ), Krefting, D ( Dagmar ), Rouilly, Vincent, Pujadas, Eva, Hullár, Béla, Balázs, Csabas, Kunszt, Peter, Podvinec, Michael, Gesing, Sandra, Glatard, Tristan, Olabarriaga, Silvia Delgado, Solomonides, Tony, Silverstein, Jonathan C, Montagnat, Johan, Gaignard, Alban, Krefting, Dagmar, Gesing, S ( Sandra ), Glatard, T ( Tristan ), Olabarriaga, S D ( Silvia Delgado ), Solomonides, T ( Tony ), Silverstein, J C ( Jonathan C ), Montagnat, J ( Johan ), Gaignard, A ( Alban ), Krefting, D ( Dagmar ), Rouilly, Vincent, Pujadas, Eva, Hullár, Béla, Balázs, Csabas, Kunszt, Peter, and Podvinec, Michael

Abstract

We report on the implementation of a software suite dedicated to the management and analysis of large scale RNAi High Content Screening (HCS). We describe the requirements identified amongst our different users, the supported data flow, and the implemented software. Our system is already supporting productively three different laboratories operating in distinct IT infrastructures. The system was already used to analyze hundreds of RNAi HCS plates.

Published
2012

16. Intravenous NPA for the treatment of infarcting myocardium early; InTIME-II, a double-blind comparison of single-bolus lanoteplase vs accelerated alteplase for the treatment of patients with acute myocardial infarction

Author

Braunwald, E., Neuhaus, K. -L., Antman, E., Chew, P., Skene, A., Wilcox, R., Ambrosioni, E., Anderson, J., Apetrei, E., Bata, I., Carrageta, M., Col, J., Dalby, A., Davies, R., Deckers, J., Eichman, D., Grande, P., Greene, R., Gurfinkel, E., Heikkilä, J., Henry, T., Hillis, D., Hochman, J., Huber, K., Kostis, J., Klinke, P., López-Sendón, J., Mckendall, G., Móller, B., Moore, P., Morris, A., Mueller, H., Östör, E., Oto, A., Ruda, M., Sadowski, Z., Schweiger, M., Sequeira, R., Shah, P., Shannon, R., Smith, B., Sobel, B., Steingart, R., Tebbe, U., Toman, J., Traboulsi, M., Vahanian, A., Warnica, J. W., Willerson, J., Deitchman, D., Davidson, L., Folgia, T., Foxley, A., Goodman, J., Hauck, C., Henry, D., Mccabe, C., Pangerl, A., Thomson, A., Wagner, M., Kennedy, J. W., Cairns, J., Demets, D., Julian, D., Simoons, M., Charlesworth, A., Easton, J. D., Ferbert, A., Feske, S., Kuhn, P., Moseley, J., Rogg, J. M., Reichmann, H., Sloan, M., von Kummer, R., Zamani, A., Coulter, S., Giugliano, R., Skene, A. M., Ardill, R., Ince, Y., Peters, A., Ward, K., Wolf, L., Curtis, N., De Brés, J., Stead, S., Watson, S., Cutler, S., Friedman, J., Helfrick, R., Williams, S., Klimovsky, J., Kumagai, S., Adams, E., Anderson, C., Bauhuber, I., Bennett, L., Biro, E., Boyce, E., Bregman, B., Carvalho, P., Ciganovic, D., Csukas, M., Cuenca, P., De Cuyper, S., Diez, P., Dijkhuizen, M., Dille-Amo, C., Gonzalez-Santis, A., Gursoy, M., Hammarstrom, K., Harasta, E., Ingman, E., Kelemen, B., Keulen, I., Koren, A., Langthaler, G., Lemaire, F., Little, I., Montalban, C., Nijssen, K., Neumueller, I., Palander, M., Pekuri, T., Persson, U., Pilz, J., Oudotova, S., Pisklakov, V., Proinov, F., Ptaszynska, A., Read, J., Retei, S., Romeyer, F., Romanini, M., Saar, L., Salein, D., Samsonov, M., Simeon-Dubach, D., Simmonds, J., Skaza, M., Skvortsova, N., Smidlova, Z., Spitzerova, H., Strijdveen, I., Szajewski, T., Ugurnal, B., Valcarce, M., van Rompaey, I., Walker, A., Zak, E., Zimova, N., Barrero, C., Beck, E., Bruno, M. L., Caccavo, A., Cagide, A., Campo, A., Cermesoni, R., Chahin, M., Dutra, O., Estrada, J., Falu, E. A., Gagliardi, J., Garre, L. E., Liprandi, A. S., Luciardi, H., Mautner, B., Muntaner, J., Nau, G., Salzberg, S., Santopinto, J., Sinisi, A., Torres, H., Eber, B., Elliott, P., Hiemetsberger, H., Juhasz, M., Kühn, P., Leisch, F., Niktardjam, M., Reisinger, J., Schmalix, G., Schuster, R., Sihorsch, K., Silberhauer, K., Slany, J., Steinbach, K., Tragl, K. H., Valentin, A., Al Shwafi, K., Dasnoy, P., De Clippel, M., de Meester, A., De Raedt, H. J. L. P., Emonts, M., Evrard, P., Eycken, M., Geboers, M., Heyndrickx, G., Lauwers, K., Mitrie, K., Pirenne, B., Renard, M., Somers, Y., Timmermans, P., Van Kuyk, M., Van Mieghem, W., Vermeulen, J., Verrostte, J. M., Albuquerque, D., Ayoub, J. C. A., Carvalho, A., Cesar, L., Gebara, O., Golin, V., Knobel, E., Leaes, P., Neto, J. A. M., Nicolau, J. C., Piegas, L. S., Rabelo, A., Rassi, A., Sila, L., Simao, A. F., Ashton, T., Baillie, H., Bhargava, R., Bota, G., Cameron, W., Chan, N., Chan, Y. K., Daly, P. A., Darcel, I., Davies, E., Desjardin, L., Dhingra, S., Ducas, J., Ervin, F. L., Fortin, C., Fowlis, R., Fulop, J., Furey, M., Gagnon, S., Gebhardt, V., Giannaccro, P., Gosselin, G., Graham, J., Grondin, F., Heath, J. W., Henderson, M., Hilton, D. R., Hiscock, J., Hui, W., Kaza, L., Kesselman, T., Kouz, S., Kucerak, M., Lahoude, N., Lamothe, M., Lebouthillier, P., Lenis, J., Levesque, P., Lopez, J. F., Lubelsky, B., Macritchie, D., Mayer, J. -P., Mcdowell, J. D., Montigny, M., Orestien-Lyall, T., Parekh, P., Pistawka, K., Price, J. B., Pruneau, G., Quinn, B., Reid, B. R., Richmond, M., Rose, B., Schuld, R., Sharma, N. K., Shetty, P., Stanton, E., Strauss, H. D., Sussex, B., Theroux, P., Turabian, M., Turner, C., Vizel, S., Walker, M., Weeks, A., Winkler, L., Zacharias, G., Zimmerman, R., Bartolucci, J., Castro, P., Diaz, M. A., Illanes, G., Potthoff, S., Sanchez, E. C., Silva, L. M., Yovanovich, J., Zanetti, F. L., Alan, D., Balázová, K., Boček, P., Cerny, J., Fischerova, B., Holub, M., Hradec, J., Janota, T., Janský, P., Kasper, J., Klimsa, Z., Motovská, Z., Pleva, L., Pluhacek, L., Pšenčka, M., Semrád, B., Spinar, J., Staněk, V., Štípal, R., Suítil, P., Vítovec, J., Wichterie, D., Widimský, P., Zeman, K., Andersen, C. B., Kriegbaum, J., Nielsen, N., Nielsen, P. E., Schou, J. B., Teesalu, R., Voitk, J., Haapamäki, H. V. H., Halkosaari, M., Härkönen, M., Jägerholm, S., Kärjä-Koskenkari, P., Karthunen, P., Kesäniemi, Y. A., Koskivirta, H., Lehto, P., Lilja, M., Paakkinen, S., Palomäki, A. K., Pietilä, K., Tuominen, J., Viopio-Pulkki, L., Ylönen, H., Adi, I., Admant, P., Akadirik, A., Alagha, Z., Alhabaj, S., Amat, G., Andre, A. A., Apffel, F., Aswad, K., Baradat, G., Bareiss, P., Barthers, F. B., Baudet, M., Baudouy, M., Bearez, E. M., Berthou, J. D., Berzin, B., Bessede, G., Blanc, J. J., Bocara, A., Bonneau, A., Bourdad, C., Bouvier, J. M., Cassagnes, J., Cassat, A., Cazaux, P., Charbonnier, B., Clementy, J., Cohen, A., Coisne, D., Colin, P., Croizier, O., D’Hautefeuille, B., D’Ivernois, C., Daumas, P. L., Dauphin, C. L., Deforet, M. F., Degand, B., Dequeker, J. L., Dickele, M. C., Dugrand, P., Durand, S., Ebagosti, A., Elharrar, C., Equine, O., Fichter, E., Flork, L., Fouche, R., Fourchard, V., Fourme, T., Fournier, P. Y., Funck, F., Galley, D., Garbarz, E., Ghadban, W., Gladin, M., Grall, J. Y., Grand, A., Gryman, R., Guillard, N., Guillo, P., Haftel, Y., Hannebicque, G., Henry, R., Huret, J. F., Janin-Magnificat, L., Jarnier, J., Joly, A., Kamal, H., Khalife, A., Roynard, J. L., Lang, M., Lapeyssonnie, A., Ledain, L., Lejeune, P., Lemetayer, L., Lepori, R., Lombart, A., Lusson, J. R., Magnin, O., Marquand, A., Martelet, M. M., Martelli, A., Mathurin, C., Mentre, B., Messager, D., Morizot, M., Mouallem, M. J., Mouhoub, O., Mycimski, C., Nallet, O., Olive, T., Pacouret, G., Palcoux, M. C., Poulard, J. E., Pruvost, A., Quiret, J. C., Richard, C., Richard, P., Rickaud, P., Riehl-Aleil, V., Rifai, A., Rocher, R., Rotreff, P., Segrestin, B., Slama, M. S., Sultan, P., Tabone, X., Talbodec, A., Tissot, M. T., Toussaint, C., Veyrat, A., Zerrouk, Z., Adamczak, M., Altmann, E., Altybernd, B., Andreassen, G., Andresen, D., Appenrodt, H., Bachmann, S., Bäcker, U., Beckert, U., Behr, H. M., Beier, W., Beier, T., Berger, D., Bernsmeier, R., Beythien, R. D., Biechl, E., Biedermann, G., Bischoff, K. O., Blerich, J., Boch, H. B., Bonzel, T., Both, A. R., Breidenbach, K., Breuer, M., Breuer, H. W. M., Brunkhorst, F. B., Bruns, A., Bundschu, H. D., Burkhardt, W., Busse, H. J., Caesar, K., Cailloud, J., Chlosta, A., Chorlanopoulos, E., Consemüller, S., Decker, W., Dichgans, M., Dick, R., Diederich, K. W., Dienst, C., Dietz, A., Dißmann, R., Ditter, H., Doering, W., Drost, H., Dundalek, E. D., Eckardt, D., Edelmann, A., Eggeling, T., Eggert, G., Eichner, R., Endres, C., Engberding, R., Engel, H. J., Faehnrich, A., Fischer, J. L., Flor, A., Forycki, F. Z. F., Froböse, H. J., Fruehauf, T., Fuchs, M., Geiser, R., Geletneky, J., Gerdes, H., Gerecke, B., Gesing, S., Gieser, H., Girth, E., Glogner, P., Glover, M., Goetz, J., Goetz, H., Göttfert, G., Gottwik, M., Gregori, B., Grieshaber, M., Großmann, C., Gruber, G., Gunold, H., Häßler, W. H., Hackenjos, B., Hader, O., Hamer, H., Harmjanz, D., Hasst, G., Haun, H., Hauptmann, K. E., Hegge, F. J., Heinze, A., Heinze, R., Henrichs, K. J., Hergenröther, H., Herrmann, F., Herzig, C., Hey, D., Hill, S., Hinzmann, S., Hoffmann, S., Höfs, T., Höhler, H., Holle, G., Höltman, B. J., Horacek, T., Hossmann, V., Hübner, F. S., Hülskamp, C., Hunecke, R., Hust, M., Jaeckh, G., Jebens, C., Jennen, E., Jost, M., Justiz, R., Kallmann, L., Kalscheur, F., Kaschner, W., Kaspar, W., Kauder, E., Keitel, B., Keller, H., Kemkes, T., Kerler, N., Kester, M., Kettner, W., Kilp, M., Kirklies, A., Klaus, A., Klein, H. H., Klenböck, J. R., Kley, H. K., Klingenbeck, R., Koch, H., Kohler, B., Kohler, J., Kolloch, R., Konermann, M., Körber, H. G., Kother, T. K., Kötter, V., Kottwitz, B., Kozariszcsuk, G., Kracht, T., Kratzsch, G., Kreft, H. U., Kreuter, G., Krönert, H., Krönig, B., Krueger, E., Krülls-Münch, J., Kuckuk, H., Kuelschbach, M., Kuhrt-Lassay, O. W., Kummerhoff, P. W., Kunevt, R., Kurth, C. U., Lang, C., Lange, C., Langhoff, R., Laskus, A., Lazarus, P., Lehmann, H. U., Lenga, P., Lengfelder, W., Leupolz, W., Limbourg, P., Loos, U., Lucanus, W., Machill, K., Mäckel, P., Mackes, K. G., Maier, S., Makowski, B., Mandok, J., Manz, M., Mäurer, W., Meier, F., Meier, J., Menges, M., Merx, W., Meurers, G., Michels, U., Mickeler, C. H., Mons, D., Moos, E., Mueller, R., Müller, G., Nast, H. P., Naumann, G., Nebelsieck, H., Neubaur, J., Niederer, W., Nitsch, J., Noack, J., Nogai, K. F. W., Oberheiden, A., Obst, R., Ochs, H. R., Odemar, F., Odenthal, H. J. B., Offers, E., Öhl, S., Ohlmeier, H. A. R. M., Patzer, P., Pech, A., Peters, U., Petry, U., Pietschmann, G. J., Pistner, W., Plappert, B., Pohlmann, W. K., Pollock, B., Presser, H. J., Przytarski, K., Puerner, K. L., Raouf, N., Reike, N., Reil, G. H., Reinhard, U., Riebeling, V., Ritzmann, M., Rödder, J., Roth, E., Rüdelstein, R., Saborowski, F., Sauter, B., Sceffler, N., Schartl, A., Schifferdecker, E., Schlotterbeck, K. P., Schmidt, J., Schmidt-Dannert, D. R., Schmidt-Klewitz, H., Schmitz, H. J., Schnebelt, T., Schneider, H. L., Schneider, F. J., Schoeller, R., Scholz, D., Schoppe, W. D., Schreiner, G., Schroeder, J., Schuh, N., Schulte, K. L., Schulze, H., Schulze, H. D., Schuster, P., Schuster, H. P., Schweizer, P., Sechtem, U., Sedlmaier, H. P., Segel, S., Sehnert, W., Seidel, F., Siedentopf, K., Simon, H., Sodomann, C. P., Solbach, C., Sorges, E., Stabenow, S., Stadler, K. P., Stammwitz, E., Stein, U., Sternberg, H., Stiepak, C., Stockmann, M., Straus, W., Striegel, H., Struch, E., Strupp, G., Taubert, T. B. T., Thoeming, B., Thoß, A., Tinnappel, J., Tomsik, H., Topp, H., Troost, S., Öberreiter, A., Uebis, R., Ungler, T., Urbaszek, W., Vöhringer, H. F., von Arnim, T., von Leitner, E. R., von Löwis of Menar, A., von Mengden, H. J., von Smekal, P., Voss, W., Wacker, P., Warning, A., Warzecha, A., Wefers, U., Wehr, M., Weigel, H., Weissthanner, F., Weller, P., Werner, M., Wette, A., Wichert, H., Wielage, T., Wiese, U., Wilbrand, T. B., Wilhelms, E., Wilmsmann, G., Wolf, F. H., Wolf, T., Wonhas, F. C. M., Zastrow, B., Zeymer, U., Ziruler, S., Ziss, W., Zölch, K. A., Zwirner, K., Becker, D., Bosko, M., Csillag, I., Ermenyi, A., Fogas, J., Heltai, K., Jánosi, A., Katona, A., Kiraly, C., Kiss, B., Kutor, G., Mizik, R., Molnar, T., Mühl, M., Nagy, D., Palacti, I., Rudas, L., Sárosi, I., Simon, K., Sitkel, E., Sydó, T., Szaboki, F., Szikla, K., Szönyi, T., Timar, S., Vándor, L., Zamolyl, K., Walsh, M., Caspi, A., Swissa, M., Badano, L., Baldacci, G., Balli, E., Banda, D., Baretta, G., Boccalatte, A., Borgatti, M. L., Branzi, A., Burelli, C., Capelletti, D., Capucci, A., Caragiulo, D., Carbonieri, E., Cassin, M., Ceci, V., Cocchieri, M., Coletta, C., Conte, E., Contini, G. M., Corsini, G., D’Annunzio, E., De Blasi, M., De Luca, I., Delciterna, F., Di Pasquale, G., Diguardo, G., Fattore, L., Ferraiuulo, G., Finardi, A., Fioretti, P. M., Giunta, G., Guiducci, U., Guzzardi, G., Horando, G., Ignone, G., Lazzaroli, A., Levantesi, D., Liberati, R., Losi, E., Macor, F., Mangiameli, S., Martines, C., Meinardi, F., Morgera, T., Morozzi, L., Mostacci, M., Naccarella, F. F., Ottani, F., Palamara, A., Pani, A., Paperini, L., Pes, R., Pesola, A., Porzio, A., Raviele, A., Ricci, S., Rosi, A., Rossi, R., Rotiroti, D., Rusconi, L., Sabino, G., Saccone, V., Sanna, A., Scaramuzzino, G., Scorcu, G. P., Semprini, F., Severini, D., Staniscia, D., Tantalo, L., Tartagni, F., Terrosu, P., Tondelli, S., Trichero, R., Uslenghi, E., Vajola, S. F., Vetrano, A., Violi, E., Zardini, P., Zingarini, G. L., Zobbi, G., Zuin, G., Kalnins, U., Cârvekülg, A., Laanoca, J., Iacis, J., Lankiene, L., Laucevicius, A., Lukoseviciute, A., Palsauskaite, R., Petrauskiene, B., Soopóld, W., Uuetoa, H., Vilks, J., Vitonyte, R., Zakke, I., Dorantes, J., Hernández, H., Jerjes, C., Leva Garza, J. L., Martinez, C., Anneveldt, A., Baars, H. F., Baldew, S. C., Bendermacher, P. E. F., Boersma, L. V. A., Bos, R. J., Breedveld, R. W., Bruggink, P. W. F., Ciampricotti, R., Darmanata, J. I., de Porto, A. E., de Weerd, G. J., Deckers, J. W., Freericks, M. P., Hillebrand, F. A., Kerker, J. P., Koenen, J. C., Kofflard, M. G. M., Liem, K. L., Liem, A. H., Linssen, G. C. M., Lionarons, R. J., Peters, J. R. M., Posma, J. P., Saat, E. W. M., Savalle, L. H., Smits, W. C. G., Suttorp, M. J., Tans, A. C., Troquay, R. P. Th., van Beek, G. J., van Boven, A. J., Van der Heijden, R., Van Hessen, A., van Langeveld, R. A. M., van Lier, T. A. R., van Loo, L. W. H., van Wijngaarden, J., van Ziejl, L. G. P. M., Veerhoek, M. J., Vermer, F., Werner, H. A., Graven, T., Klykken, B., Meyerdieks, O., Omland, T. M., Otterstad, J. E., Pedersen, T., Rød, R., Banaszewski, M., Bednarkiewicz, Z., Bojarski, G., Ceremuzyñski, L., Czestochowska, E., Gajewski, M., Galewicz, M., Gorski, J., Grabczewska, Z. S., Gruchaka, M., Janicki, K., Janion, M., Jaworska, K., Jezewska, M., Kakol, J., Kizciuk, M., Kleinrok, A., Kolodziej, P., Komorowski, P., Konopka, A., Kopaczewski, J., Korecki, J., Kornacewicz-Jach, Z., Kowalewski, M., Kratochwil, D., Krolczyk, J., Krzminska-Pakula, M., Kurek, P., Kurowski, M., Kurpesa, M., Kurzawski, J., Kwiecien, R., Lenartowski, L., Lewandowski, M., Loboz-Grudzieñ, K., Luczak, G., Maliñski, A., Michalski, M., Musial, W., Nartowicz, E., Nowicka, A., Odyniec, A., Pasyk, S., Prastowski, W., Przybylski, A., Raczynska, A., Rodzik, J., Romanowski, M., Rynkiewicz, A., Rzyman, M., Sidorowicz, A., Sledziona, M., Sobiczewski, W., Sobkowicz, B., Sobolewska, J., Sokalski, L., Stepinska, J., Sterlinski, M., Stopinski, M., Świątecka, G., Szpernal, Z., Tarnowska, H., Trzos, E., Ujda, M., Wierzchowiecki, M., Wodynska, T., Wojciechowski, D., Wrabec, K., Wrzesinski, K., Zuk, P., Albuquergue, A., Costa, A., Cunha, D., Ferreira, D., Ferreira, R., Gaog Leiria, J. M., Pimenta, A., Rufino, E., Vasconcelos, J., Aldica, M., Balanescu, S., Bruckner, I. V., Capalneanu, R., Florescu, N., Georgescu, C. S., Cherasim, L., Ginshina, C., Merenta, A., Parvu, O., Radutiu, S., Savulescu, I., Vita, I., Averkov, O., Bokarev, I. N., Gratsiansky, N., Grigoriev, Y., Gruzdev, A., Kakhnovsky, I., Kheevehuk, T. V., Khrustalev, O., Kobalava, Y., Konoratieva, T. B., Koukline, Vladimir, Martiouchov, S., Pavlikova, E., Poskotinov, I., Rogalev, K., Sinopainikov, A., Syrkin, A., Tereschenko, S. T., Yavelov, I., Zavolghin, S., Čurilla, E., Kohn, R., Kovář, F., Murín, J., Poliačik, P., Drinovec, I., Horvat, M., Krivec, B., Markež, J., Pareznik, R., Pehnec, Z., Resman, J., Sifrer, F., Skale, R., Trinkaus, D., Voga, G., Baig, M. M. E., Blomerus, P., Botha, B. P., Burgess, L., Duncan, D., Duncan, D. I., Gillmer, D., Govender, N., Jardine, R. J., Kok, A., Manga, P., Naidu, R. K., Rajput, M. C., Ranjith, N., Roos, J. S., Snyders, F. A., Steingo, L., Stern, A., Tayob, F. Z., Vythilingum, S., Alonso-Orcajo, N., Arribas Jimenez, A., Ayestaran, J. I., Balsera, B. B. G., Barras, C., Castro, A., Cobo, N., Duque, A., Garcia, M. J., Goiriena, P., Gonzalez-Valdayo, M., Gulias Lopez, J. M., Jimenez Gomez, P., Lopez Garanda, V., Martín Santos, F., Nogueira, R., Pabon Osuna, P., Ponce De Leon, E., Quesada Dorador, A., Paya Serrano, R., Rodriguez, L., Rodriguez, M., Rubio, F., Ruiz-Salmeron, R., Solar, J., Toquero, J., Velasco, J., Vilar Herrero, V., Vizcaino, M., Wancisidor, X., Basilier, E., Birgersdotter, V., Björnsdotter, E., Bjurman, A., Hagström, D., Hallin, I., Hansen, O., Hemmingson, L. O., Lundkvist, L., Lycksell, M., Möller, B., Nolgard, P., Sjölund, G., Stjerna, A., Angehrn, W., de Benedetti, E., Diethelm, M., Gallino, A., Plebani, G., Vögelin, H. P., Wojtyna, W., Akgöz, H., Akgün, G., Akyürek, O., Batur, M. K., Bayata, S., Deger, N., Emel, O., Gürgün, C., Korkmaz, M. E., Kozan, O., Kumbasar, D., Muderrisoglu, H., Nisanci, Y., Ozin, B., Ozsaruhan, O., Payzin, S., Postaci, N., Sozcuer, H., Tamci, B., Topuzoglu, F., Türkoglu, C., Tutar, E., Ulucam, M., Ulusoy, T., Umman, B., Yalçinkaya, S., Yesil, M., Zoghi, M., Adams, P. C., Ahir, S., Ahsan, A. J., Akhtar, J., Albers, C. J., Al-Khafaji, M. N., Anderson, N., Bailey, R. J., Bain, R. J. I., Basu, A., Beal, A., Boyle, R. M., Brown, N., Campbell, S., Card, D., Cross, S. J., Davies, P., Davis, E. T. L., Dean, J. W., Deaner, A., Devine, M. A., Dhawan, J., Doig, J. C., Dubrey, S., Dunn, P. G., Dwight, J., Ecob, R., Fitzpatrick, H., Fletcher, S., Francis, C. M., Gershlick, A. H., Glennon, P. E., Goodfield, N. E., Grabau, W. J., Gray, M., Gray, K. E., Heath, J., Hendry, W. G., Highland, J., Hogg, K., Irving, J. B., James, M. A., Jennings, K., Joy, M., Kadr, H. H., Kahn, S., Keeling, P. J., Keir, P. M., Kemp, T. M., Kinaird, J., Kinsey, C., Knowles, K., Kooner, J. S., Lahiri, A., Lawson, C., Lewis, R., Macdermott, A. F. N., Mackay, A., Macleod, D. C., Mccance, A. J., Morrison, A., Mortimer, M., Mulvey, D., Murphy, J. J., Murray, S., Muthusamy, R., Myers, A., Nicolson, V. G., Northridge, D., Odemuyiwa, S., Oldroyd, K. G., Oliver, R. M., Pell, A. C. H., Pohl, J. E. F., Price, B., Quereshi, N., Rae, A. P., Reader, S., Reid, D. S., Reynolds, G. W., Robinson, A., Robson, R. H., Rodger, J. C., Rodrigues, E., Rose, E. L., Rowlands, D. B., Rowley, J. M., Rozkovec, A., Shreeve, J., Siklos, P., Smith, R. H., Sneddon, J. F., Somasundram, U., Squire, I., Stephens, J. D., Stephens-Lloyd, A., Strand, J. M., Stuart, J., Sutaria, N., Swan, J., Tait, G. W., Thomas, R. D., Thompson, M. A., Tildesley, G., Travill, C. M., Treadgold, J. A., Trelawney, J. M. S., Turner, D., Vallance, B. D., Wallbridge, D., Weissberg, P. L., White, E., Wicks, M., Wilcox, R. G., Wilkinson, P., Wiltshire, J. E., Wright, A., Andrea, B., Attassi, K., Bahr, R., Banas, J., Baran, K., Belknap, M., Bensman, M., Bertolet, B., Besley, D., Bethala, V., Betzu, R., Bhalla, R., Bhargava, M., Binder, A., Birkhead, R., Bodine, K., Brewer, D., Carey, S., Chengot, M., Coppola, J., Cragg, D., D’Arcy, B., Denny, D. M., Dilorenzo, P., Dixon, E., Doorey, A., Doty, D., Doty, W., Drossner, M., Eisenberg, P., Falco, T., Feldman, R., Freman, I., Frey, M., Garcia, J., Glassman, J., Goldman, S., Gomez, M., Gonzalez, M., Goodfield, P., Gottlieb, S., Grech, D., Hack, T., Haffey, T., Hanson, J., Havranek, E., Hermany, P., Hernandez, H., Herron, R., Hession, W., Hines, J., Hundley, R., Jacobs, W. C., Jerjes-Sanchez, C., Jerome, S., Josephson, R., Kalan, J., Kawalsky, D., Khan, A., Kmetzo, K., Kraemer, M., Lader, E., Landis, J., Lash, J., Leber, R., Leimbach, W., Leiva Garza, J. -L., Maddox, W., Magorien, R., Mahapatra, S., Mantecon, I., Mendelson, R., Miklin, J., Milas, J., Miller, R., Molk, B., Monrad, E. S., Morrison, J., Morse, H., Neustel, M., Nichols, D., Niederman, A., Nygaard, T., O’Connor, R., O’Riordan, W., Obermueller, S., Palmeri, S., Patel, R., Paul, T., Phiambolis, T., Piana, R., Polansky, B., Polinski, W., Ponce, G., Ribeiro, P., Roccario, E., Rogers, C. P., Rogers, W., Rosenblatt, A., Runyon, J. P., Scheel, F., Schmidt, P., Schneider, R., Schwartz, H., Shelhamer, L., Sheridan, F., Shine, W., Shook, T., Siskind, S., Slama, R., Spear, E., Stouffer, G., Strunk, B., Thadani, U., Timmis, G., Trautloff, R., Tse, A., Wohl, B., Zarren, H., Zucker, R., Kuster, F., and Pardie, J. P.

Subjects
Male, Risk, Infusions, medicine.medical_treatment, Myocardial Infarction, Bolus lytic therapy, Acute myocardial infarction, Tissue plasminogen activator, Thrombolytic drug, Double-Blind Method, Fibrinolytic Agents, medicine, Humans, Thrombolytic Therapy, Myocardial infarction, Infusions, Intravenous, Stroke, Aged, business.industry, ST elevation, Lanoteplase, Emergency department, Middle Aged, medicine.disease, Survival Analysis, Regimen, Relative risk, Anesthesia, Tissue Plasminogen Activator, Female, Intracranial Hemorrhages, Cardiology and Cardiovascular Medicine, business, Intravenous, medicine.drug
Abstract

AIMS To compare the efficacy and safety of lanoteplase, a single-bolus thrombolytic drug derived from alteplase tissue plasminogen activator, with the established accelerated alteplase regimen in patients presenting within 6 h of onset of ST elevation acute myocardial infarction. METHODS AND RESULTS 15,078 patients were recruited from 855 hospitals worldwide and randomized in a 2:1 ratio to receive either lanoteplase 120 KU. kg(-1)as a single intravenous bolus, or up to 100 mg accelerated alteplase given over 90 min. The primary end-point was all-cause mortality at 30 days and the hypothesis was that the two treatments would be equivalent. By 30 days, 6.61% of alteplase-treated patients and 6.75% lanoteplase-treated patients had died (relative risk 1.02). Total stroke occurred in 1.53% alteplase- and 1.87% lanoteplase-treated patients (ns); haemorrhagic stroke rates were 0.64% alteplase and 1.12% lanoteplase (P=0.004). The net clinical deficit of 30-day death or non-fatal disabling stroke was 7.0% and 7.2%, respectively. By 6 months, 8.8% of alteplase-treated patients and 8.7% of lanoteplase-treated patients had died. CONCLUSION Single-bolus weight-adjusted lanoteplase is an effective thrombolytic agent, equivalent to alteplase in terms of its impact on survival and with a comparable risk-benefit profile. The single-bolus regimen should shorten symptoms to treatment times and be especially convenient for emergency department or out-of-hospital administration.

Published
2000

17. Granular security for a science gateway in structural bioinformatics

Author

Gesing, S., Grunzke, R., Balaskó, A., Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., Fels, G., Herres-Pawlis, S., Kacsuk, P., Kozlovszky, M., Jens Krüger, Packschies, L., Schäfer, P., Schuller, B., Schuster, J., Steinke, T., Szikszay Fabri, A., Wewior, M., Müller-Pfefferkorn, R., and Kohlbacher, O.

20. MoSgrid: Progress of workflow driven chemical simulations

Author

Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., Fels, G., Gesing, S., Grunzke, R., Sonja Herres-Pawlis, Kohlbacher, O., Krüger, J., Lang, U., Packschies, L., Müller-Pfefferkorn, R., Schäfer, P., Schuster, J., Steinke, T., Warzecha, K. -D, and Wewior, M.

24. A data driven science gateway for computational workflows

Author

Grunzke, R., Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., Gesing, S., Herres-Pawlis, S., Kohlbacher, O., Krüger, J., Kruse, M., Ralph Müller-Pfefferkorn, Schäfer, P., Schuller, B., Steinke, T., and Zink, A.

25. Molecular simulation grid

Author

Krüger Jens, Birkenheuer Georg, Blunk Dirk, Breuers Sebastian, Brinkmann André, Fels Gregor, Gesing Sandra, Grunzke Richard, Kohlbacher Oliver, Kruber Nico, Lang Ulrich, Packschies Lars, Müller-Pfefferkorn Ralph, Herres-Pawlis Sonja, Schäfer Patrick, Schmalz Hans-Günther, Steinke Thomas, Warzecha Klaus-Dieter, and Wewior Martin

Subjects
Information technology, T58.5-58.64, Chemistry, QD1-999
Published
2011
Full Text
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26. A Secure Cloud-based Platform to Host Healthcare Applications

Author

Pierantoni, G., Kiss, T., Terstyanszky, G., Dang, H.V., Delgado Olabarriaga, S., Tuler de Olivera, M., Yigzaw, K. Y., Belika, J. G., Krefting, D., Penzel, T., Gesing, S., and Sandra Gesing

Subjects
HealthCare, Privacy, Security, Cloud applications
Abstract

Digital technologies, such as Big Data analytics, artificial intelligence, cloud and high-performance computing are presenting new opportunities to transform healthcare systems, increase connectivity of hospitals and other providers, and therefore potentially and significantly improve patient care. However, such networked computing infrastructures also raise significant cybersecurity risks, especially in the healthcare domain, where protecting sensitive personal information is of paramount importance. Project ASCLEPIOS aims at strengthening the trust of users in cloud-based healthcare services by utilizing trusted execution environment and several modern cryptographic approaches such as attribute based encryption, searchable encryption, functional encryption to build a cloud-based e-health framework that protects users’ privacy, prevents both internal and external attacks, verifies the integrity of medical devices before application, and runs privacy-preserving data analytics on encrypted data. The project investigates modern encryption techniques and their combination in order to provide increased security of e-health applications that are then presented towards end-users utilizing a cloud-based platform. Although some topics such as security and privacy are already investigated through block-chain related technologies, it has been decided that the selected approaches would be more suitable for these particular challenges. In order to prototype its security services, ASCLEPIOS develops and deploys three large-scale healthcare demonstrators, provided by three leading hospitals from Europe. These demonstrators are rooted in the practice-based problems and applications provided by the project’s healthcare partners. The Amsterdam University Centers, University of Amsterdam, plans to improve stroke hyper-acute care through secure information sharing on a cloud computing platform to improve patient management. Additionally, they are also building prediction models to enable earlier discharge of patients from hospitals with lower risk factors. Charité Berlin plans to improve inpatient and outpatient sleep medication by remotely controlling the quality of the collected data and transferring it on-line for further analysis. Finally, the Norwegian Centre for e-health Research, University Hospital of North Norway is developing a system for privacy-preserving monitoring and benchmarking of antibiotics prescription of general practitioners. The common characteristics of these three scenarios are the increased demand for high levels of security in data transfer, storage and privacy preserving analytics on cloud infrastructures. In order deploy, operate and further develop these applications to increase their security with the ASCLEPIOS framework, a cloud computing testbed is being setup. The testbed uses state-of-the-art technologies for cloud application deployment and run-time orchestration in order to ensure the optimized deployment and execution of the demonstrator applications. As the data sources do not require the local execution (albeit in one case data may remain on the data source) of processing, there is no need for fog or edge computing, but the testbed is based on private OpenStack cloud computing infrastructures and utilizes the MiCADO framework which is compatible with different containers such as Docker and Kubernetes. The project started only recently, and currently it is in the early stages of systems design and specification. This presentation will provide a short introduction to the ASCLEPIOS project and its demonstrators and will present early results of the currently ongoing requirements specification and platform design processes.

Published
2019

27. Enabling modular design of an application-level auto-scaling and orchestration framework using tosca-based application description templates

Author

Deslauriers, J., Kiss, T., Pierantoni, G., Gesmier, G., Terstyanszky, G., Stankovski, V, Gesing, S., and Sandra Gesing

Subjects
container orchestration, docker swarm, kubernetes, MiCADO, TOSCA
Abstract

This paper presents a novel approach to writing TOSCA templates for application reusability and portability in a modular auto-scaling and orchestration framework (MiCADO). The approach defines cloud resources as well as application containers in a flexible and generic way, and allows for those definitions to be extended with specific properties related to a desired container orchestrator chosen at deployment time. The approach is demonstrated in a proof-of-concept where only a minor change was required to a previously used application template in order to achieve the successful deployment and lifecycle management of the popular web authoring tool Wordpress on a new realization of the MiCADO framework featuring a different container orchestrator.

Published
2019

28. High-level Description of Cloud Applications using TOSCA

Author

Terstyanszky, G., Kiss, T., Gesmier, G., Pierantoni, G., Gesing, S., Atkinson, M., Sandra Gesing, and Prof Malcolm Atkinson

Abstract

Public sector organizations and SMEs are increasingly considering using cloud services in their everyday activities. At the one hand on-demand access to cloud services in a flexible and elastic way could result in significant cost savings due to more efficient and convenient utilization. Further it can also replace large investment costs with long-term operational costs. On the other hand, the take up of cloud computing by the public sector and Small- and Medium-size Enterprises (SME) is still relatively low due to limited application-level flexibility and shortages in cloud specific skills. To meet these requirements a generic framework is needed to support public sector organizations and SMEs to run large variety of applications in the cloud in a cost effective, flexible and seamless way. To address these challenges the European funded COLA (Cloud Orchestration at the Level of Application) [1] project is designing and developing a modular architecture called MiCADO (Microservices-based Cloud Application-level Dynamic Orchestrator) [2]. It provides optimized deployment and run-time orchestration for cloud applications. MiCADO can manage applications considering their specific deployment, execution, scalability and security requirements. To further address this challenge COLA uses TOSCA (Topology and Orchestration Specification for Cloud Applications [3] to describe applications to be executed in the cloud. Application developers can create so called Application Description Templates (ADT) to specify and submit their applications to the cloud through MiCADO. ADTs define two key properties of applications: topologies and policies. There are two approaches to define ADTs: using either command-line interfaces or graphical user interfaces. Command-line interface requires deep knowledge of the TOSCA specification and good YAML knowledge. Since application developers in the public sector organizations and at SMEs may not have this knowledge COLA’s priority is providing a GUI–based environment to enable application developers to describe their applications. The project investigated several GUI-based TOSCA development environments such as, OpenTOSCA Winery [4] and Alien 4 Cloud [5]. Winery generates XML-based specification of application topologies. The current Winery version automatically translates the XML-based TOSCA specifications into YAML to make them compatible with the latest TOSCA specification. Since each translation has its own limitations, some TOSCA features that are required in COLA, are lost in translation. The other limitation of Winery is that it does not support the definition of TOSCA policy specifications. Fig. 1 presents a simple topology template developed in Winery. Although Alien 4 Cloud supports the definition of cloud applications through a GUI environment, the generated description is not fully TOSCA compliant and cannot be parsed with most widely used TOSCA parsers. Considering the above listed limitations, COLA is developing a GUI-based environment to support application specification in TOSCA YAML v1.0. The extra feature of this environment will be a wide range support for policy specification, for example enabling development of deployment, execution, scalability and security policies.

Published
2018

29. Job-queuing and auto-scaling in container-based cloud environments

Author

Abu Oun, O., Tamas Kiss, Gesing, S., Atkinson, M., and Sandra Gesing

Subjects
cloud computing, container technologies, Docker Swarm, JQueuer, autoscaler, MiCADO
Abstract

Many applications process large quantities of data that takes significant time and requires big amount of compu- tational resources. Optimising the execution of such applications in a cloud computing environment by keeping costs at minimum but still completing the task by a set deadline has paramount importance. As container-based technologies are becoming more widespread, support for job-queuing and auto-scaling in such environments is becoming important. Current container tech- nologies, such as Docker or Kubernetes provide limited support in this area. This paper presents JQueuer and CAutoScaler, a couple of cloud-independent solutions that offer job-queuing and automated scalability at the level of containers. Applying these solutions leads to more cloud-aware applications providing transparent auto-scaling for end-users and optimising execution time and costs. Business and science gateways will benefit from using an orchestrator combined with JQueuer and CAutoScaler since it will provide the layers needed to auto-scale the containers and to batch/sweep the jobs from a queue depending on a user- defined policy.

30. Unleashing quantum algorithms with Qinterpreter: bridging the gap between theory and practice across leading quantum computing platforms.

Author

Contreras-Sepúlveda W, Villegas-Martínez BM, Gesing S, Sánchez-Mondragón JJ, Sánchez-Pérez JC, Vidales-Basurto CA, Escobedo-Alatorre JJ, Torres-Palencia AD, Palillero-Sandoval O, Licea-Rodriguez J, Lozano-Crisóstomo N, García-Melgarejo JC, and Palacios-Perez EN

Abstract

Quantum computing is a rapidly emerging and promising field with the potential to transform various research domains including drug design, network technologies, and sustainable energy solutions. Due to the inherent complexity and divergence from classical computing, several major quantum computing libraries have been developed to implement quantum algorithms, namely IBM Qiskit, Amazon Braket, Cirq, PyQuil, and PennyLane. These libraries enable quantum simulations on classical computers and execution on corresponding quantum hardware, such as Qiskit programs on IBM quantum computers. Despite the variations among these platforms, the core concepts remain the same. One notable challenge is the absence of a Python-based quantum interpreter to connect these five frameworks, a gap that remains to be fully addressed. In response, our work introduces a tool called Qinterpreter, accessible through a user-friendly web interface, the Quantum Science Gateway QubitHub, which operates alongside Jupyter Notebooks. Built using the Python Object-Oriented Programming System, Qinterpreter unifies the five well-known quantum libraries into a single framework. Designed as an educational tool for students and researchers entering the quantum domain, Qinterpreter enables the straightforward development and execution of quantum circuits across such platforms. This work highlights the quantum programming versatility and accessibility of Qinterpreter and underscores our ultimate goal of pervading Quantum Computing through younger, less specialized, and diverse cultural and national communities., Competing Interests: The authors declare that they have no competing interests. Sandra Gesing is an Academic Editor for PeerJ Computer Science., (© 2024 Contreras-Sepúlveda et al.)

Published
2024
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31. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.

Author

Labbé F, Abdeladhim M, Abrudan J, Araki AS, Araujo RN, Arensburger P, Benoit JB, Brazil RP, Bruno RV, Bueno da Silva Rivas G, Carvalho de Abreu V, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Figueiredo Gontijo N, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERGR, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler JL, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACA, Minx P, Miranda JC, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Horacio Pereira M, Nobrega Pitaluga A, Proveti Olmo R, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant'Anna MRV, Scherer SE, Secundino NFC, Shoue DA, da Silva Moraes C, Gesto JSM, Souza NA, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JT, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, and McDowell MA

Subjects
Animals, Humans, Genomics, Phlebotomus parasitology, Psychodidae parasitology, Leishmania genetics, Leishmaniasis, Cutaneous
Abstract

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Published
2023
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32. A survey of the state of the practice for research software in the United States.

Author

Carver JC, Weber N, Ram K, Gesing S, and Katz DS

Abstract

Research software is a critical component of contemporary scholarship. Yet, most research software is developed and managed in ways that are at odds with its long-term sustainability. This paper presents findings from a survey of 1,149 researchers, primarily from the United States, about sustainability challenges they face in developing and using research software. Some of our key findings include a repeated need for more opportunities and time for developers of research software to receive training. These training needs cross the software lifecycle and various types of tools. We also identified the recurring need for better models of funding research software and for providing credit to those who develop the software so they can advance in their careers. The results of this survey will help inform future infrastructure and service support for software developers and users, as well as national research policy aimed at increasing the sustainability of research software., Competing Interests: Daniel S. Katz and Sandra Gesing are Academic Editors for PeerJ CS., (©2022 Carver et al.)

Published
2022
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33. Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.

Author

Austin CC, Bernier A, Bezuidenhout L, Bicarregui J, Biro T, Cambon-Thomsen A, Carroll SR, Cournia Z, Dabrowski PW, Diallo G, Duflot T, Garcia L, Gesing S, Gonzalez-Beltran A, Gururaj A, Harrower N, Lin D, Medeiros C, Méndez E, Meyers N, Mietchen D, Nagrani R, Nilsonne G, Parker S, Pickering B, Pienta A, Polydoratou P, Psomopoulos F, Rennes S, Rowe R, Sansone SA, Shanahan H, Sitz L, Stocks J, Tovani-Palone MR, and Uhlmansiek M

Abstract

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research. These guidelines include recommendations for clinicians, researchers, policy- and decision-makers, funders, publishers, public health experts, disaster preparedness and response experts, infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations), and other potential users. These guidelines include recommendations for researchers, policymakers, funders, publishers and infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations). Several overarching themes have emerged from this document such as the need to balance the creation of data adherent to FAIR principles (findable, accessible, interoperable and reusable), with the need for quick data release; the use of trustworthy research data repositories; the use of well-annotated data with meaningful metadata; and practices of documenting methods and software. The resulting document marks an unprecedented cross-disciplinary, cross-sectoral, and cross-jurisdictional effort authored by over 160 experts from around the globe. This letter summarises key points of the Recommendations and Guidelines, highlights the relevant findings, shines a spotlight on the process, and suggests how these developments can be leveraged by the wider scientific community., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 Austin CC et al.)

Published
2021
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34. Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.

Author

Austin CC, Bernier A, Bezuidenhout L, Bicarregui J, Biro T, Cambon-Thomsen A, Carroll SR, Cournia Z, Dabrowski PW, Diallo G, Duflot T, Garcia L, Gesing S, Gonzalez-Beltran A, Gururaj A, Harrower N, Lin D, Medeiros C, Méndez E, Meyers N, Mietchen D, Nagrani R, Nilsonne G, Parker S, Pickering B, Pienta A, Polydoratou P, Psomopoulos F, Rennes S, Rowe R, Sansone SA, Shanahan H, Sitz L, Stocks J, Tovani-Palone MR, and Uhlmansiek M

Abstract

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research. These guidelines include recommendations for researchers, policymakers, funders, publishers and infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations). Several overarching themes have emerged from this document such as the need to balance the creation of data adherent to FAIR principles (findable, accessible, interoperable and reusable), with the need for quick data release; the use of trustworthy research data repositories; the use of well-annotated data with meaningful metadata; and practices of documenting methods and software. The resulting document marks an unprecedented cross-disciplinary, cross-sectoral, and cross-jurisdictional effort authored by over 160 experts from around the globe. This letter summarises key points of the Recommendations and Guidelines, highlights the relevant findings, shines a spotlight on the process, and suggests how these developments can be leveraged by the wider scientific community., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Austin CC et al.)

Published
2020
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35. The challenges of theory-software translation.

Author

Jay C, Haines R, Katz DS, Carver JC, Gesing S, Brandt SR, Howison J, Dubey A, Phillips JC, Wan H, and Turk MJ

Subjects
Engineering, Humans, Knowledge, Research Personnel, Computing Methodologies, Software
Abstract

Background : Software is now ubiquitous within research. In addition to the general challenges common to all software development projects, research software must also represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process of theory-software translation is robust is essential to maintaining the integrity of the science resulting from it, and yet there has been little formal recognition or exploration of the challenges associated with it. Methods : We thematically analyse the outputs of the discussion sessions at the Theory-Software Translation Workshop 2019, where academic researchers and research software engineers from a variety of domains, and with particular expertise in high performance computing, explored the process of translating between scientific theory and software. Results : We identify a wide range of challenges to implementing scientific theory in research software and using the resulting data and models for the advancement of knowledge. We categorise these within the emergent themes of design, infrastructure, and culture, and map them to associated research questions. Conclusions : Systematically investigating how software is constructed and its outputs used within science has the potential to improve the robustness of research software and accelerate progress in its development. We propose that this issue be examined within a new research area of theory-software translation, which would aim to significantly advance both knowledge and scientific practice., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Jay C et al.)

Published
2020
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36. Advances in distributed computing with modern drug discovery.

Author

Banegas-Luna AJ, Imbernón B, Llanes Castro A, Pérez-Garrido A, Cerón-Carrasco JP, Gesing S, Merelli I, D'Agostino D, and Pérez-Sánchez H

Subjects
Algorithms, Animals, Computing Methodologies, Humans, Software, Time Factors, Computational Chemistry methods, Computer Simulation, Drug Discovery methods
Abstract

Introduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms. Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD). Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.

Published
2019
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37. Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

Author

Arshad J, Hoffmann A, Gesing S, Grunzke R, Krüger J, Kiss T, Herres-Pawlis S, and Terstyanszky G

Abstract

Background: In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows., Significance: Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows., Conclusions: We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

Published
2016
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38. Developing science gateways for drug discovery in a grid environment.

Author

Pérez-Sánchez H, Rezaei V, Mezhuyev V, Man D, Peña-García J, den-Haan H, and Gesing S

Abstract

Background: Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources., Results: To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows., Conclusions: Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

Published
2016
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39. From the desktop to the grid: scalable bioinformatics via workflow conversion.

Author

de la Garza L, Veit J, Szolek A, Röttig M, Aiche S, Gesing S, Reinert K, and Kohlbacher O

Subjects
Reproducibility of Results, Computational Biology methods, Computer Communication Networks, Microcomputers, Software, Workflow
Abstract

Background: Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks. There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free -an aspect that could potentially drive away members of the scientific community., Results: We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources., Conclusions: Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We strongly believe that our efforts not only decrease the turnaround time to obtain scientific results but also have a positive impact on reproducibility, thus elevating the quality of obtained scientific results.

Published
2016
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41. Portals and Web-Based Resources for Virtual Screening.

Author

Krüger J, Thiel P, Merelli I, Grunzke R, and Gesing S

Subjects
Computer Simulation, Databases, Chemical, Humans, Internet, Ligands, Models, Molecular, Molecular Docking Simulation, User-Computer Interface, Drug Discovery methods, Proteins chemistry, Proteins metabolism
Abstract

Virtual screening for active compounds has become an essential step within the drug development pipeline. The computer based prediction of compound binding modes is one of the most time and cost efficient methods for screening ligand libraries and enrich results of potential drugs. Here we present an overview about currently available online resources regarding compound databases, docking applications, and science gateways for drug discovery and virtual screening, in order to help structural biologists in choosing the best tools for their analysis. The appearance of the user interface, authentication and security aspects, data management, and computational performance will be discussed. We anticipate a broad overview about currently available solutions, guiding computational chemists and users from related fields towards scientifically reliable results.

Published
2016
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42. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.

Author

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, Madey G, Collins FH, and Lawson D

Subjects
Animals, Biological Ontologies, Gene Expression Profiling, Genetic Variation, Genome, Humans, Insecticide Resistance, Internet, Invertebrates genetics, Metabolic Networks and Pathways genetics, Databases, Genetic, Disease Vectors, Genomics
Abstract

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2015
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43. The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations.

Author

Krüger J, Grunzke R, Gesing S, Breuers S, Brinkmann A, de la Garza L, Kohlbacher O, Kruse M, Nagel WE, Packschies L, Müller-Pfefferkorn R, Schäfer P, Schärfe C, Steinke T, Schlemmer T, Warzecha KD, Zink A, and Herres-Pawlis S

Abstract

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.

Published
2014
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44. Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives.

Author

Merelli I, Pérez-Sánchez H, Gesing S, and D'Agostino D

Subjects
Humans, Precision Medicine, Software, Biomedical Research, Computational Biology methods, Data Mining methods, Delivery of Health Care
Abstract

The explosion of the data both in the biomedical research and in the healthcare systems demands urgent solutions. In particular, the research in omics sciences is moving from a hypothesis-driven to a data-driven approach. Healthcare is additionally always asking for a tighter integration with biomedical data in order to promote personalized medicine and to provide better treatments. Efficient analysis and interpretation of Big Data opens new avenues to explore molecular biology, new questions to ask about physiological and pathological states, and new ways to answer these open issues. Such analyses lead to better understanding of diseases and development of better and personalized diagnostics and therapeutics. However, such progresses are directly related to the availability of new solutions to deal with this huge amount of information. New paradigms are needed to store and access data, for its annotation and integration and finally for inferring knowledge and making it available to researchers. Bioinformatics can be viewed as the "glue" for all these processes. A clear awareness of present high performance computing (HPC) solutions in bioinformatics, Big Data analysis paradigms for computational biology, and the issues that are still open in the biomedical and healthcare fields represent the starting point to win this challenge.

Published
2014
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45. Performance studies on distributed virtual screening.

Author

Krüger J, Grunzke R, Herres-Pawlis S, Hoffmann A, de la Garza L, Kohlbacher O, Nagel WE, and Gesing S

Subjects
Databases, Protein, Drug Discovery methods, Molecular Docking Simulation methods, Protein Kinase Inhibitors chemistry, Protein Kinases chemistry
Abstract

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.

Published
2014
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47. Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi.

Author

Gesing S, Schindler D, and Nowrousian M

Subjects
Gene Deletion, Gene Library, Real-Time Polymerase Chain Reaction, Ascomycota genetics, Fungi genetics, Gene Expression Profiling methods, Gene Expression Regulation, Fungal, Nucleic Acid Hybridization methods
Abstract

Ascomycetes differentiate four major morphological types of fruiting bodies (apothecia, perithecia, pseudothecia and cleistothecia) that are derived from an ancestral fruiting body. Thus, fruiting body differentiation is most likely controlled by a set of common core genes. One way to identify such genes is to search for genes with evolutionary conserved expression patterns. Using suppression subtractive hybridization (SSH), we selected differentially expressed transcripts in Pyronema confluens (Pezizales) by comparing two cDNA libraries specific for sexual and for vegetative development, respectively. The expression patterns of selected genes from both libraries were verified by quantitative real time PCR. Expression of several corresponding homologous genes was found to be conserved in two members of the Sordariales (Sordaria macrospora and Neurospora crassa), a derived group of ascomycetes that is only distantly related to the Pezizales. Knockout studies with N. crassa orthologues of differentially regulated genes revealed a functional role during fruiting body development for the gene NCU05079, encoding a putative MFS peptide transporter. These data indicate conserved gene expression patterns and a functional role of the corresponding genes during fruiting body development; such genes are candidates of choice for further functional analysis., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2013
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48. The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora.

Author

Gesing S, Schindler D, Fränzel B, Wolters D, and Nowrousian M

Subjects
Cell Nucleus chemistry, DNA, Fungal chemistry, DNA, Fungal genetics, Fungal Proteins genetics, Gene Deletion, Genes, Fungal, Genetic Complementation Test, Mass Spectrometry, Microarray Analysis, Molecular Chaperones genetics, Molecular Sequence Data, Protein Interaction Mapping, Sequence Analysis, DNA, Sordariales genetics, Two-Hybrid System Techniques, Fungal Proteins metabolism, Genes, Essential, Histones metabolism, Molecular Chaperones metabolism, Sordariales growth & development
Abstract

Ascomycetes develop four major types of fruiting bodies that share a common ancestor, and a set of common core genes most likely controls this process. One way to identify such genes is to search for conserved expression patterns. We analysed microarray data of Fusarium graminearum and Sordaria macrospora, identifying 78 genes with similar expression patterns during fruiting body development. One of these genes was asf1 (anti-silencing function 1), encoding a predicted histone chaperone. asf1 expression is also upregulated during development in the distantly related ascomycete Pyronema confluens. To test whether asf1 plays a role in fungal development, we generated an S. macrospora asf1 deletion mutant. The mutant is sterile and can be complemented to fertility by transformation with the wild-type asf1 and its P. confluens homologue. An ASF1-EGFP fusion protein localizes to the nucleus. By tandem-affinity purification/mass spectrometry as well as yeast two-hybrid analysis, we identified histones H3 and H4 as ASF1 interaction partners. Several developmental genes are dependent on asf1 for correct transcriptional expression. Deletion of the histone chaperone genes rtt106 and cac2 did not cause any developmental phenotypes. These data indicate that asf1 of S. macrospora encodes a conserved histone chaperone that is required for fruiting body development., (© 2012 Blackwell Publishing Ltd.)

Published
2012
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49. Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway.

Author

Herres-Pawlis S, Birkenheuer G, Brinkmann A, Gesing S, Grunzke R, Jäkel R, Kohlbacher O, Krüger J, and Dos Santos Vieira I

Subjects
Computer Simulation, Health Services Research methods, Information Dissemination methods, Molecular Conformation, Workflow, Guanidine chemistry, Information Storage and Retrieval methods, Internet, Models, Molecular, Science, User-Computer Interface, Zinc chemistry
Abstract

The new science gateway MoSGrid (Molecular Simulation Grid) enables users to submit and process molecular simulation studies on a large scale. A conformational analysis of guanidine zinc complexes, which are active catalysts in the ring-opening polymerization of lactide, is presented as an example. Such a large-scale quantum chemical study is enabled by workflow technologies. Two times 40 conformers have been generated, for two guanidine zinc complexes. Their structures were optimized using Gaussian03 and the energies processed within the quantum chemistry portlet of the MoSGrid portal. All meta- and post-processing steps have been performed in this portlet. All workflow features are implemented via WS-PGRADE and submitted to UNICORE.

Published
2012

50. Workshop series IWSG-Life.

Author

Gesing S and Krüger J

Subjects
Biological Science Disciplines, Health Services Research methods, Information Dissemination methods, Information Storage and Retrieval methods, Internet, User-Computer Interface
Published
2012

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