Publications

This is an index of papers, slide decks, and other assorted material on GC3Pie. Most recent contributions are listed first.

If you would like to add your contributions here, please send a message to the GC3Pie mailing-list (or use the web interface).

GC3Pie overviews

The following slides and papers provide an overview of GC3Pie and its features. (Most recent entries first.)

• GC3Pie: orchestrating large-scale execution of scientific applications. Presentation of GC3Pie and its features, especially focusing on the GC3Pie backend for EasyBuild. Held at the HPC-CH forum. June 11, 2015.
• GC3Pie: orchestrating large-scale execution of scientific applications. Presentation of GC3Pie and its features at the HPC-CH forum. June 18, 2014.
• Presentation of GC3Pie and GC3Libs (PDF) at the a private meeting with the developers of iBRAIN2/3 (later renamed to screeningBee), May 2012.
• GC3Pie: A Python framework for high-throughput computing (MAFFIOLETTI, Sergio, and Riccardo Murri). Proceedings of the EGI Community Forum 2012/EMI Second Technical Conference (EGICF12-EMITC2). 26-30 March, 2012. Munich, Germany. Published online at, id. 143. Vol. 1. 2012.
• Presentation of GC3Pie and GC3Libs (PDF) at the NorduGrid conference 2011.

Programming examples

The following slides focus on GC3Libs programming. (Most recent entries first.)

• Global Optimization with GC3Pie (PDF). Poster presented at the EuroSciPy 2013 conference, introducing the GC3Pie numerical optimizer.
• Computational workflows with GC3Pie (PDF). Poster presented at the EGI Community Forum 2012.
• Computational workflows with GC3Pie (PDF). Poster presented at the EuroSciPy 2011 conference.
• Introduction to GC3Pie and its programming model (HTML, PDF); slides presented at the Advanced School on High Performance and Grid Computing at ICTP Trieste.
• Introduction to GC3Libs programming (HTML, PDF); slides presented at the SMSCG Project meeting 2011.
• Introduction to GC3Libs programming (HTML, PDF); slides presented at a private meeting with the Selectome developers.

Use of GC3Pie in scientific applications

These papers and presentations cover specific tools built on top of GC3Pie, or applications of GC3Pie to research in a specific domain. (Most recent entries first.)

• TRAL: Tandem repeat annotation library (Schaper, E., Korsunsky, A., Messina, A., Murri, R., Pečerska, J., Stockinger, H., … & Anisimova, M.). Bioinformatics, btv306 (2015).
• Selectome update: quality control and computational improvements to a database of positive selection (Moretti, S., Laurenczy, B., Gharib, W. H., Castella, B., Kuzniar, A., Schabauer, H., … & Robinson-Rechavi, M.). Nucleic acids research, 42(D1), D917-D921, 2014.
• Wireless Mesh Networks and Cloud Computing for Real Time Environmental Simulations (Kropf, P., Schiller, E., Brunner, P., Schilling, O., Hunkeler, D., & Lapin, A.). In Recent Advances in Information and Communication Technology (pp. 1-11). Springer International Publishing. * Real-Time Environmental Monitoring for Cloud-Based Hydrogeological Modeling with HydroGeoSphere (Lapin, A., Schiller, E., Kropf, P., Schilling, O., Brunner, P., Kapic, A. J., … & Maffioletti, S.). In High Performance Computing and Communications, 2014 IEEE 6th Intl Symp on Cyberspace Safety and Security, 2014 IEEE 11th Intl Conf on Embedded Software and Syst (HPCC, CSS, ICESS), 2014 IEEE Intl Conf on (pp. 959-965). IEEE, August 2014.
• Thermal and Hydrological Response of Rock Glaciers to Climate Change: A Scenario Based Simulation Study (Apaloo, J.). University of Waterloo, Canada, 2014.
• Parameter estimation of complex mathematical models of human physiology using remote simulation distributed in scientific cloud (Kulhanek, T., Mateják, M., Silar, J., & Kofranek, J.). In Biomedical and Health Informatics (BHI), 2014 IEEE-EMBS International Conference on (pp. 712-715). IEEE, June 2014.
• Towards a swiss national research infrastructure (Kunszt, P., Maffioletti, S., Flanders, D., Eurich, M., Bohnert, T., Edmonds, A., … & Schiller, E.). arXiv preprint arXiv:1404.7608.
• User Interaction and Data Management for Large Scale Grid Applications. Journal of Grid Computing (Costantini, A., Gervasi, O., Zollo, F., & Caprini, L.), 12(3), 485-497, 2014.
• Application of large-scale computing infrastructure for diverse environmental research applications using GC3Pie (Maffioletti, S., Dawes, N., Bavay, M., Sarni, S., & Lehning, M.). In EGU General Assembly Conference Abstracts (Vol. 15, p. 13222). April 2013.
• gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution (Moretti, S., Murri, R., Maffioletti, S., Kuzniar, A., Castella, B., Salamin, N., … & Stockinger, H.). Studies in health technology and informatics, 175, 59-68 (2012).
• A Grid execution model for Computational Chemistry Applications using the GC3Pie framework and AppPot (Costantini, A., Murri, R., Maffioletti, S., Rampino, S., & Laganà, A.). Computational Science and Its Applications–ICCSA 2012. Springer Berlin Heidelberg, 2012. 401-416.
• Running GAMESS jobs with ggamess. Slides presented at a Baldridge Research Group meeting, Sept 2012.
• The MP2 binding energy of the ethene dimer and its dependence on the auxiliary basis sets: a benchmark study using a newly developed infrastructure for the processing of quantum chemical data (Glöß, A., Brändle, M. P., Klopper, W., & Lüthi, H. P.). Molecular Physics, 110(19-20), 2523-2534 (2012).
• Three tools for high-throughput computing with GAMESS (PDF). Slides presented at a Baldridge Research Group meeting, May 2011.
• Enabling High-Throughput Computational Chemistry on the Grid (PDF). Poster presented at the EGI User Forum 2011.
• GRunDB: a tool for validating QM algorithms in GAMESS-US (PDF). Slides presented at the Swiss Grid Day 2010.
• GC3Pie and related tools for high-throughput computational chemistry (PowerPoint PPT slides). Presentation held at the Databases in Quantum Chemistry workshop, September 22-25, 2010 in Zaragoza, Spain.