Outreach

Robbie Joosten. “How good is my model? And can it be improved?”, Computational Biotechnology at the Nanoscale, Faridabad, India, February 15-20, 2016.

Alexandre Bonvin. “West-Life: A virtual research environment for structural biology”. International Symposium on Grid and Cloud Computing, Tapei, Taiwan, March 15-18th, 2016.

Alexandre Bonvin. “High resolution modelling with 3D blurry images”. Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, March 15th, 2016.

Antonio Rosato. “The MoBrain Competence Center for Translational Research from Molecule to Brain”, EGI Conference 2016 - Opening science in Europe and in the World, Amsterdam, The Netherlands, April 4-6, 2016.

Alexandre Bonvin. “Information-driven modelling of biomolecular complexes”. INSTRUCT practical course on “Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition”, Utrecht, the Netherlands, April 11-15, 2016.

Antonio Rosato. “Molecular dynamics for NMR-based protein structure refinement”, INSTRUCT practical course on “Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition”, Utrecht, the Netherlands, April 11-15, 2016.

Alexandre Bonvin. “Sense and simplicity in HADDOCK scoring: Lessons from CAPRI”. CAPRI meeting, Tel Aviv, April 17-20, 2016.

Alexandre Bonvin. “Integrative modelling of biomolecular complexes using HADDOCK2.2”. BioExcel workshop, EBI, Hinxton UK, May 3-4, 2016.

Alexandre Bonvin. “Integrative modelling of biomolecular complexes”, School on molecular modelling for life science, Pula, Italy, June 6-10, 2016.

Alexandre Bonvin. “Structure, affinity and specificity riddles in biomolecular interactions”. 13th Annual Meeting of the Bioinformatics Italian Society - keynote lecture, Salerno, Italy, June 15-17, 2016.

Alexandre Bonvin. EMBO Global Exchange Lecture Course on “Structural and Biophysical Methods for Biological Macromolecules in Solution”, Suwon, South Korea, June 19-26, 2016.

Alexandre Bonvin. “Integrative modelling of biomolecular complexes: High-resolution modelling with blurry 3D images”, Summer Workshop by Biochemistry Division of Korean Chemical Society, KAIST, Daejon, South Korea, June 27, 2016.

Robbie Joosten. “Validation & optimisation: From a solved structure to the final model”, CCP4/APS School in Macromolecular Crystallography, Argonne, IL, USA, June 21-29, 2016.

Gregor Chojnowski. "Automated Protein Model Building with ARP/wARP 7.4", CCP4/APS School in Macromolecular Crystallography, Argonne, IL, USA, June 21-29, 2016.

Gregor Chojnowski. "ARP/wARP Automatic Building", CCP4 SPring-8 school: From data processing to structure refinement and beyond January 23 – 27, 2017.

Alexandre Bonvin. EMBO practical course on “Integrative modelling of biomolecular complexes”, Barcelona, Spain, July 4-9, 2016.

Alexandre Bonvin. EMBO practical course on “Multidimensional NMR in Structural Biology”, Joachimsthal, Germany, July 11-15, 2016.

Alexandre Bonvin. “Integrative modelling of biomolecular complexes”, Institute Pasteur course on integrative structural biology, Paris, France, July 20-21, 2016

Marco Verlato at the DI4R conference, Krakow, Sept. 2016, Federated accelerated computing platforms for EGI

Anastassis Perrakis, “From ARP/WARP to PDB_REDO: a short history and perspectives”. Joint International Conference of the HeCrA and the HSCCB, Athens, Greece, October 7-9, 2016.

Wouter Touw (NKI), “Validation-driven model optimisation”. X-Ray Methods in Structural Biology, Cold Spring Harbour, NY, USA, October 10-15, 2016.

Alexandre Bonvin, “West-Life: Structural biology in the clouds”. iNext user meeting, Alcala de Henares, Spain, October 19-21, 2016.

Robbie Joosten, “PDB_REDO: What’s (i)NEXT? ”. iNext user meeting, Alcala de Henares, Spain, October 19-21, 2016.

Alexandre Bonvin. “Structure, affinity and specificity riddles in biomolecular interactions”. Modelling of protein interaction conference, Lawrence KS, USA, October 27-29, 2016.

Alexandre Bonvin. “High-resolution, integrative modelling of biomolecular complexes from fuzzy data”, Helmholtz Training Course on Integrative Structural Biology, Braunschweig, Germany, November 7-11, 2016

Antonio Rosato. “INSTRUCT, a distributed infrastructure for integrated structural biology”, FAIR Data Management: best practices and open issues, Firenze, Italia, November 14-15, 2016.

Alexandre Bonvin. “High-resolution, integrative modelling of biomolecular complexes from fuzzy data”, EMBO conference on Molecular Machines: Integrative Structural and Molecular, November 20-23, 2016

Bart van Beusekom (NKI). “Homology-based restraints improve low-resolution protein structure models”, CHAINS 2016: Chemistry Matters for the Future, Veldhoven, The Netherlands, December 6-8, 2016.

Robbie Joosten. “Model validation and optimisation”, DLS-CCP4 Data Collection and Structure Solution Workshop, Oxford, UK, December 13-20, 2016.

Jose Miguel de la Rosa. INSTRUCT practical course: Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition, Utrecht, Netherlands, April 11-15, 2016

Jose Maria Carazo. INSTRUCT practical course: Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition, Utrecht, Netherlands, April 11-15, 2016

Jose Miguel de la Rosa. “Cryo EM solving the structure of macromolecular complexes: A hands on workshop One day practical workshop with Scipion”, International Symposium on Grids and Clouds", Taipei, Taiwan, March 14-17, 2016

Jose Maria Carazo. “Soft validation in cryo EM”, Weizmann Center, Tel Aviv, Israel, March 2016

Laura del Caño & Jesus Cuenca. “CryoEM: From Biomedical impact to Cloud deployment”, EGI Conference 2016, Amsterdam, Netherlands, April 8, 2016

Jose Maria Carazo. “Cryo Electron Microscopy: The EM RESOLUTION REVOLUTION”, Leloir Foundation, Buenos Aires, Argentina, July 2016

Jose Maria Carazo. “The EM RESOLUTION REVOLUTION”, Universidade de São Paulo, Sao Paulo, Brazil, July 2016

Jose Maria Carazo. “The Electron Microscopy “Revolution” and the need of new data validation and data integration approaches”, National Institute of Medical Sciences and Nutrition Salvador Zubirán (INCMNSZ), Mexico DF, August 2016

Jose Maria Carazo. “Pervasive data processing and information integration in Cryo Electron Microscopy”, EGI Conference 2016, New York, USA, August 2016

Lucia Banci. “Cellular Structural Biology: from structures to functional processes”, 42nd Conference on "In the Vanguard of Structural Biology: Revolutionizing Life Sciences", 4-7 October 2016, Naito, Japan.

Lucia Banci. “Cellular Processes Described at Atomic Resolution by NMR” , 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS), 21-26 August 2016, Kyoto, Japan

Lucia Banci. “NMR in Cellular Structural Biology: combining atomic resolution with the cellular context” British Biophysical Society, Biennial Meeting, 6-8 July 2016, Liverpool, UK

Lucia Banci. “NMR in Cellular Structural Biology: from structures to functional processes”, Euromar 2016, 3-7 July 2016, Aarthus, Denmark.

Lucia Banci. “Spectral Assignment and Structure Calculation”, EMBO Global Exchange Lecture Course, 19-26 June 2016, Suwon, Korea.

Lucia Banci. “What we learn from motions of the biomolecules?”, 14th International School of Biological Magnetic Resonance, 7-17 May 2016, Erice, Italy.

Lucia Banci. “NMR in Cellular Structural Biology and few cool ways to do NMR” Scientific Symposium: 50 Cool Ways to Do NMR, 11 April 2016, Frankfurt, Germany.

Martyn Winn. “What to do with all that Data” at “Advanced Data Collection for High Resolution cryoEM: How to make the most of your National Facility Visit”, Biochemical Society Training Day, Diamond National EM Facility (eBIC), 6 September 2016

Martyn Winn. “Life Sciences work in STFC” at IBM-STFC workshop, IBM Yorktown, 13 April 2016

Chris Morris. "DI4U" DI4R: The first cross e-infrastructure event for users, Krakow, 28-30 September 2016

Alexandre Bonvin. High-resolution integrative modelling of biomolecular complexes from fuzzy data. ISGC 2017, Taiwan

Alexandre Bonvin. The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes harvesting EGI GPGPU resources. ISGC 2017, Taiwan (https://indico4.twgrid.org/indico/event/2/session/30/contribution/4)

Jose Maria Carazo. Image processing in cryo Electron Microscopy (cryo EM): Analyzing reliability and quality. ISCG 2017, Taiwan. (https://indico4.twgrid.org/indico/event/2/session/30/contribution/134)

Jose Maria Carazo. Image Processing in cryoEM: Open problems and current perspectives. ISGC 2017, Taiwan

Jose Maria Carazo. Image Processing in cryoEM: Quality checks. Netherland Center for Nanoscopi, Laiden, 27 January 2017

Antonio Rosato. Molecular dynamics of proteins in the cloud. ISCG 2017, Taiwan. (https://indico4.twgrid.org/indico/event/2/session/31/contribution/38)

Marco Verlato. EGI federated platforms supporting accelerated computing. ISCG 2017, Taiwan. (https://indico4.twgrid.org/indico/event/2/session/47/contribution/6)

Jose Maria Carazo. Image processing in cryoEM: Validation. Max F. Perutz Laboratories. Dept. of Structural and Computational Biology, University of Vienna, 16 March 2017

Poster Presentation - M. Trellet, GROMACS in the Clouds: A Portative User-friendly Interface Bridged to Grid- computing Resources (ISGC 2017, Taiwan)

Poster Presentation - A. Krenek, Virtualized Web Portals in EGI Federated Cloud (ISGC 2017, Taiwan)

Poster presentation - 1st iNEXT User Meeting, Alcala de Henares, Madrid, Spain. J.M. de la Rosa-Trevin, A. Quintana, L. del Cano, A. Zaldívar, R. Melero, I. Foche, J. Gutiérrez, J. Gómez-Blanco, J. Burguet-Castell, J. Cuenca- Alba, V. Abrishami, J. Vargas, J. Otón, G. Sharov, J.L. Vilas, J. Navas, P. Conesa, M. Kazemi, R. Marabini, C.O.S. Sorzano, J.M. Carazo. SCIPION: Integrating 3DEM software

Poster Presentation - M. Trellet, J. Schaarschmidt, G.C.P. van Zundert, Z. Kurkcuoglu, A.S.J. Melquiond and A.M.J.J. Bonvin. Integrative modelling goes HPC/HTC. F1000Research, 5:2216 (poster) (2016)

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB and Carazo JM (2016) The Electron Microscopy eXchange (EMX) initiative. Journal of Structural Biology. Elsevier BV 194(2): 156–163. doi: 10.1016/j.jsb.2016.02.008.

van Zundert GCP, Trellet M, Schaarschmidt J, Kurkcuoglu Z, David M, Verlato M, Rosato A and Bonvin AMJJ (2017) The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes. Journal of Molecular Biology. Elsevier BV 429(3): 399–407. doi: 10.1016/j.jmb.2016.11.032.

van Zundert GCP and Bonvin AMJJ (2016) Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. Journal of Structural Biology. Elsevier BV 195(2): 252–258. doi: 10.1016/j.jsb.2016.06.011.

Spiliotopoulos D, Kastritis PL, Melquiond ASJ, Bonvin AMJJ, Musco G, Rocchia W and Spitaleri A (2016) dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. Frontiers in Molecular Biosciences. Frontiers Media SA 3. doi: 10.3389/fmolb.2016.00046.

Not open Access:

Sala D, Giachetti A, Luchinat C and Rosato A (2016) A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. Journal of Biomolecular NMR. Springer Nature 66(3): 175–185. doi: 10.1007/s10858-016-0065-6.


Title

Audience

Number of participants

Countries represented

Second Advanced methods for the integration of diverse structural data with NMR data

Structural Biology community

20

Czech Republic, France, Germany, Italy,

Netherlands, Singapore, Spain, UK, USA

First I2PC-FEI “hands on” course on image processing applied to the structural characterization of biological macromolecules

Structural Biology community

20

Austria, Czech Republic, Denmark, France, Germany, Netherlands, Italy, Spain, UK

Cryo EM Solving the Structure of Macromolecular Complexes: A Hands-on Workshop at International Symposium on Grids and Clouds 2016

New user community

20

India, Malaysia, Netherlands, Spain, Taiwan

From 2D images to 3D structures: A practical course on Electron Microscopy Single Particle Analysis

Structural Biology community

22

Czech Republic, Slovenia, Denmark, UK, France, Netherlands, Germany, Switzerland, Latvia, Italy, Spain

Cryo-EM Workshop at International Symposium on Grids and Clouds 2017

New user community

40

Czech Republic, France, India, Italy, Malaysia, Netherlands, Spain, Taiwan

West-Life Hackathon

West-Life Developers

10

Czech Republic, France, Italy, Netherlands, Spain, UK

DIRAC Workshop for West-Life

West-Life Developers

12

Czech Republic, Italy, Netherlands, Spain, UK

Hands-On course on Cloud Orchestration

Developer community

9

Czech Republic, Germany, Greece, Netherlands, Romania, Spain, UK