diff --git a/source/Community/BoincPublications.htm.erb b/source/Community/BoincPublications.htm.erb
deleted file mode 100644
index 76f8a905..00000000
--- a/source/Community/BoincPublications.htm.erb
+++ /dev/null
@@ -1,248 +0,0 @@
----
-title: "Gridcoin - BOINC Publications"
-description: "A list of published scientific papers related to BOINC and volunteer distributed computing."
----
-
-
-
-
-
-
BOINC Publications
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Technical papers involving BOINC
-
- -
- C.B. Ries and V. Grout, Code Generation Approaches for an Automatic Transformation of the Unified Modeling Language to the Berkeley Open Infrastructure for Network Computing Framework, in Proc. International Conference on Soft Computing and Software Engineering (SCSE'13), San Francisco (USA): SF State University
-
- -
- C.B. Ries, C. Schröder, and V. Grout, Model-based Generation of Workunits, Computation Sequences, Series and Service Interfaces for BOINC based Projects, in Proc. International Conference on Software Engineering Research and Practice (SERP'12), part of WORLDCOMP'12, USA, Las Vegas, July, 2012
-
- -
- C.B. Ries, C. Schröder, and V. Grout, A UML Profile for the Berkeley Open Infrastructure for Network Computing (BOINC), in Proc. IEEE Conference on Computer Applications and Industrial Electronics (ICCAIE 2011), Malaysia, Penang, December, 2011
-
- -
- C.B. Ries, C. Schröder, and V. Grout, Generation of an Integrated Development Environment (IDE) for Berkeley Open Infrastructure for Network Computing (BOINC), in Proc. Seventh Collaborative Research Symposium on Security, E-learning, Internet and Networking (SEIN 2011), Germany, Furtwangen, October, 2011
-
- -
- A Modeling Language Approach for the Abstraction of the Berkeley Open Infrastructure for Network Computing (BOINC) Framework, Christian Benjamin Ries, Thomas Hilbig, and Christian Schröder, in Proc. IEEE International Multiconference on Computer Science and Information Technology (IMCSIT), Poland, Wisla, October, 2010
-
- -
- Correlated Resource Models of Internet End Hosts Eric Heien, Derrick Kondo, David P. Anderson. 31st International Conference on Distributed Computing Systems (ICDCS), Minneapolis, Minnesota, USA, 2011.
-
- -
- ComsolGrid - A framework for performing large-scale parameter studies using Comsol Multiphysics and Berkeley Open Infrastructure for Network Computing (BOINC). Christian Benjamin Ries and Christian Schröder, COMSOL Multiphysics Conference, Proceedings of the COMSOL Conference, ISBN: 978-0-9825697-6-4, France, Paris, 2010
-
- -
- Discovering Statistical Models of Availability in Large Distributed Systems: An Empirical Study of SETI@home. Bahman Javadi, Derrick Kondo, Jean-Marc Vincent, David P. Anderson. IEEE Transactions on Parallel and Distributed Computing.
-
- -
- Oded Nov, Ofer Arazy, and David P. Anderson. Crowdsourcing for science: understanding and enhancing SciSourcing contribution. The Changing Dynamics of Scientific Collaborations, workshop at CSCW 2010, Savannah GA, Feb. 7 2010.
-
- -
- Exploiting Non-Dedicated Resources for Cloud Computing. Artur Andrzejak, Derrick Kondo and David P. Anderson. To appear in the 12th IEEE/IFIP Network Operations & Management Symposium (NOMS 2010), Osaka, Japan April 19-23, 2010.
-
- -
- A Communication Framework for Fault-tolerant Parallel Execution. Nagarajan Kanna, Jaspal Subhlok, Edgar Gabriel, Eshwar Rohit and David Anderson. The 22nd International Workshop on Languages and Compilers for Parallel Computing, Newark, Delaware, Oct 8-10 2009.
-
- -
- Computing Low Latency Batches with Unreliable Workers in Volunteer Computing Environments. Eric M. Heien, David P. Anderson, and Kenichi Hagihara. To appear, Journal of Grid Computing.
-
- -
- Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. Trilce Estrada, Michela Taufer, David Anderson. To appear, Journal of Grid Computing.
-
- -
- Mining for Statistical Models of Availability in Large-Scale Distributed Systems: An Empirical Study of SETI@home. Bahman Javadi, Derrick Kondo, Jean-Marc Vincent, David P. Anderson. 17th Annual Meeting of the IEEE/ACM International Symposium on Modelling, Analysis and Simulation of Computer and Telecommunication Systems, Sept 21-23 2009, London.
-
- -
- Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing Using Constraint Optimization. James Atlas, Trilce Estrada, Keith Decker, Michela Taufer. ICCS 2009.
-
- -
- Cost-Benefit Analysis of Cloud Computing versus Desktop Grids. Derrick Kondo, Bahman Javadi, Paul Malecot, Franck Cappello and David Anderson. 18th International Heterogeneity in Computing Workshop, May 25 2009, Rome.
-
- -
- EmBOINC: An Emulator for Performace Analysis of BOINC Projects. Trilce Estrada, Michela Taufer, Kevin Reed, David Anderson. 3rd Workshop on Desktop Grids and Volunteer Computing Systems (PCGrid 2009), May 29, 2009, Rome.
-
- -
- Celebrating Diversity in Volunteer Computing. David P. Anderson and Kevin Reed. Hawaii International Conference on System Sciences (HICSS), January 5-8, 2009. (Best Paper award)
-
- -
- Ensuring Collective Availability in Volatile Resource Pools via Forecasting. Artur Andrzejak, Derrick Kondo, and David P. Anderson. 19th IFIP/IEEE International Workshop on Distributed Systems: Operations and Management (DSOM 2008), Samos Island, Greece, September 22-26, 2008.
-
- -
- On Correlated Availability in Internet-Distributed Systems. Derrick Kondo, Artur Andrzejak, and David P. Anderson. 9th IEEE/ACM International Conference on Grid Computing (Grid 2008), Tsukuba, Japan, Sept 29 - Oct 1 2008.
-
- -
- Performance Evaluation of Scheduling Policies for Volunteer Computing. Derrick Kondo, David P. Anderson and John McLeod VII. 3rd IEEE International Conference on e-Science and Grid Computing. Banagalore, India, December 10-13 2007.
-
- -
- Local Scheduling for Volunteer Computing. David P. Anderson and John McLeod VII. Workshop on Large-Scale, Volatile Desktop Grids (PCGrid 2007) held in conjunction with the IEEE International Parallel & Distributed Processing Symposium (IPDPS), March 30, 2007, Long Beach.
-
- -
- Designing a Runtime System for Volunteer Computing. David P. Anderson, Carl Christensen and Bruce Allen. Supercomputing '06 (The International Conference for High Performance Computing, Networking, Storage and Analysis), Tampa, November 2006.
-
- -
- The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects. Trilce Estrada, David A. Flores, Michela Taufer, Patricia J. Teller, Andre Kerstens, David P. Anderson. Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), p. 88.
-
- -
- The Computational and Storage Potential of Volunteer Computing. David P. Anderson and Gilles Fedak IEEE/ACM International Symposium on Cluster Computing and the Grid, Singapore, May 16-19, 2006.
-
- -
- High-Performance Task Distribution for Volunteer Computing. David P. Anderson, Eric Korpela, Rom Walton First IEEE International Conference on e-Science and Grid Technologies. 5-8 December 2005, Melbourne
-
- -
- Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. M. Taufer, D. Anderson, P. Cicotti, C.L. Brooks III. From 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) Heterogeneous Computing Workshop. April 4 2005, Denver CO.
-
- -
- Developing Distributed Computing Solutions Combining Grid Computing and Public Computing. Jakob Gregor Pedersen & Christian Ulrik Søttrup. Master's thesis from University of Copenhagen. March 2005. (Describes tools for transparently moving jobs between Condor and BOINC.)
-
- -
- Distributed MD4 Password Hashing with Grid Computing Package BOINC. Stephen Pellicer, Yi Pan and Minyi Guo. Grid and Cooperative Computing – GCC 2004. Third International Conference Wuhan, China, October 21-24, 2004 Proceedings.
-
- -
- BOINC: A System for Public-Resource Computing and Storage. David P. Anderson. 5th IEEE/ACM International Workshop on Grid Computing. November 8, 2004, Pittsburgh, USA.
-
-
-
-
-
-
-
Project-specific papers
-
- -
- Science@Duquesne: Structure of Aqueous Sodium Perchlorate Solutions, Ignacio J. General, Eliana K. Asciutto and Jeffry D. Madura, J. Phys. Chem. B, 2008, 112 (48), pp 15417–15425.
-
- -
- Distributed computing and farm management with application to the search for heavy gauge bosons using the ATLAS experiment at the LHC. Lopez-Perez, Juan Antonio. PhD thesis, Jan. 2008.
-
- -
- Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Myers, D. S., A. L. Bazinet and M. P. Cummings. 2008. Pages 71-85. In Talbi, E.-G. and A. Zomaya (Eds.) Grids for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing. John Wiley & Sons, New York.
-
- -
- Gene Sequence Alignment on a Public Computing Platform. Stephen Pellicer, Nova Ahmed, Yi Pan, and Yao Zheng. Proceedings of the 2005 International Conference on Parallel Processing Workshops (ICPP@'05), 2005.
-
- -
- The Challenge of Volunteer Computing With Lengthy Climate Model Simulations. Carl Christensen, Tolu Aina and David Stainforth. First IEEE International Conference on e-Science and Grid Technologies. 5-8 December 2005, Melbourne
-
- -
- Reporting@Home: Delivering Dynamic Graphical Feedback to Participants in Community Computing Projects. Stuart Ozer, David E. Kim, David Baker (Microsoft Research Technical report MSR-TR-2007-17).
-
-
-
-
-
-
-
-
-
Other papers on volunteer computing
-
- -
- A. Marosi, G. Gombas, Z. Balaton, P. Kacsuk. SZTAKI Desktop Grid: Building a Scalable, Secure Platform for Desktop Grid Computing. CoreGRID Technical Report TR-100.
-
- -
- M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, and P.J. Teller: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. Proceedings of the International Workshop on Principles of Advanced and Distributed Simulation 2007 (PADS'07), June 2007, San Diego, California, USA.
-
- -
- M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, R. Zamudio, P.J. Teller, R. Armen, and C.L. Brooks III: Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. Proceedings of the First Workshop on Large-Scale, Volatile Desktop Grids (PCGrid'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
-
- -
- SLINC: A Framework for Volunteer Computing, James Baldassari, David Finkel, and David Toth, Proceedings of the 18th IASTED International Conference on Parallel and Distributed Computing and Systems - PDCS 2006, November 13-15, 2006, Dallas, Texas, USA.
-
- -
- BOINC on JXTA by Marcin Cieslak (Thesis from Technical University of Wroclaw, Poland).
-
- -
- Silaghi, G. , Araujo, F. , Domingues, P. , Silva, L. M. , Arenas, A. Defeating Colluding Nodes in Desktop Grid Computing Platforms. in Proceedings of the 22nd IPDPS conference, PCGrid2008 workshop, Miami, USA, April 2008.
-
- -
- D. Toth The Impact of Multi-Core Architectures on Task Retrieval Policies for Volunteer Computing. Proceedings of The 20th IASTED International Conference on Parallel and Distributed Computing and Systems - PDCS 2008, November 16-18, 2008, pp. 330-335, Orlando, Florida, USA.
-
- -
- D. Toth and D. Finkel Increasing the Amount of Work Completed by Volunteer Computing Projects with Task Distribution Policies. Proceedings of the 2nd Workshop on Desktop Grids and Volunteer Computing Systems (PCGrid 2008), in conjunction with IPDPS'08, April 18, 2008, Miami, Florida, USA.
-
- -
- D. Toth Volunteer Computing with Video Game Consoles. Proceedings of the 6th WSEAS International Conference on Software Engineering, Parallel and Distributed Systems (SEPADS 2007), February 16-19, 2007, Corfu, Greece.
-
- -
- D. Toth and D. Finkel Characterizing Resource Availability for Volunteer Computing and its Impact on Task Distribution Methods. Proceedings of the 6th WSEAS International Conference on Software Engineering, Parallel and Distributed Systems (SEPADS 2007), February 16-19, 2007, Corfu, Greece.
-
- -
- D. Toth and D. Finkel. A Comparison of Techniques for Distributing File-based Tasks for Public-Resource Computing. Proceedings of The 17th IASTED International Conference on Parallel and Distributed Computing and Systems - PDCS 2005, November 14-16, 2005, pp. 398-403, Phoenix, Arizona, USA.
-
- -
- Kan Watanabe, Masaru Fukushi, Susumu Horiguchi. Optimal Spot-checking to minimize the Computation Time in Volunteer Computing. Proceedings of the 22nd IPDPS conference, PCGrid2008 workshop, Miami, USA, April 2008.
-
-
-
-
-
-
-
diff --git a/source/Community/ProjectPublications.htm.erb b/source/Community/ProjectPublications.htm.erb
deleted file mode 100644
index 1ca78ab3..00000000
--- a/source/Community/ProjectPublications.htm.erb
+++ /dev/null
@@ -1,634 +0,0 @@
----
-title: "Gridcoin - Project Publications"
-description: "A list of scientific papers published by BOINC projects."
----
-
-
-
-
-
-
Project Publications
-
-
-
-
-
-
-
-
-
-
-
-
Brief
-
Science research projects typically publish their results in scientific journals.
-
Preliminary results are often published in conferences.
-
In the academic world, the scientific contribution of a project is measured largely by the number of its publications, and the prestige of the journals and conferences in which they appear (high-prestige journals include Nature, Science, and PNAS).
-
We encourage BOINC volunteers to support projects that make a major scientific contribution.
-
Keep in mind that doing research and publishing papers may take several years, so newer projects will naturally have few or no publications.
- The following scientific papers have resulted from BOINC-based projects (this list does not include papers about volunteer computing or about BOINC itself; those are here).
-
-
-
-
-
-
- -
- James Murphy, David Sexton, David Barnett, Gareth Jones, Mark Webb, Matthew Collins & David Stainforth, Quantification of modelling uncertainties in a large ensemble of climate change simulations, Nature, 430, pp. 768-772, August 2004.
-
- -
- D. A. Stainforth, T. Aina, C. Christensen, M. Collins, N. Faull, D. J. Frame, J. A. Kettleborough, S. Knight, A. Martin, J. M. Murphy, C. Piani, D. Sexton, L. A. Smith, R. A. Spicer, A. J. Thorpe & M. R. Allen, Uncertainty in predictions of the climate response to rising levels of greenhouse gases, Nature, 433, pp. 403-406, January 2005.
-
- -
- D. J. Frame, B. B. B. Booth, J. A. Kettleborough, D. A. Stainforth, J. M. Gregory, M. Collins, and M. R. Allen, Constraining climate forecasts: The role of prior assumptions, Geophysical Review Letters, 32, May 2005.
-
- -
- C. Piani, D. J. Frame, D. A. Stainforth, and M. R. Allen, Constraints on climate change from a multi-thousand member ensemble of simulations, Geophysical Review Letters, 32, December 2005.
-
- -
- P. Pall, M.R. Allen, D.A. Stone, Testing the Clausius-Clapeyron constraint on changes in extreme precipitation under CO2 warming. Climate Dynamics, 23:4, pp. 351-363, August 2006.
-
- -
- M. Collins and S. Knight (Eds.), Ensembles and probabilities: a new era in the prediction of climate change, Phil. Trans. R. Soc. A, Print: 1364-503X, Online: 1471-2962, 2007.
-
- -
- C.G. Knight, S.H.E. Knight, N. Massey, T. Aina, C. Christensen, D.J. Frame, J.A. Kettleborough, A. Martin, S. Pascoe, B. Sanderson, D.A. Stainforth, M.R. Allen, Association of parameter, software and hardware variation with large scale behavior across 57,000 climate models, PNAS, July 2007.
-
- -
- B. M. Sanderson, R. Knutti, T. Aina, C. M. Christensen, N. E. Faull, D. J. Frame, W. J. Ingram, C. Piani, D. A. Stainforth, D. A. Stone and M. R. Allen. Constraints on model response to greenhouse gas forcing and the role of sub-grid scale processes, Journal of Climate, in press, 2007.
-
- -
- C. Piani, T. Aina, C. Christensen, D. Frame, N. Faull and M. Allen. Regional probabilistic climate forecasts from a multi-thousand, multi-model ensemble of simulations, Journal of Geophysical Research, accepted, 2007.
-
- -
- D. J. Frame, N. E. Faull, M. M. Joshi & M. R. Allen, Probabilistic climate forecasts and inductive problems, Philosophical Transactions of the Royal Society A, 2007.
-
- -
- D. Ackerley, E. J. Highwood, and D. J. Frame, Quantifying the effects of perturbing the physics of an interactive sulfur scheme using an ensemble of GCMs on the climateprediction.net platform, J. Geophys. Res., 114, D01203, January 2009.
-
- -
- D.J. Frame, T. Aina, C.M. Christensen, N. E. Fall, S.H.E. Knight, C. Piani, S.M. Rosier, K. Yamazaki, Y. Yamazaki and M.R. Allen, The climateprediction.net BBC climate change experiment: design of the coupled model ensemble, Philosophical Transactions of The Royal Society A, 367, pp.855-870, 2009.
-
- -
- H. Fowler, D. Cooley, S. Sain and M. Thurston, Detecting change in UK extreme precipitation using results from the climateprediction.net BBC climate change experiment, 2010, Extremes DOI 10.1007/s10687-010-0101-y.
-
- -
- Pardeep Pall, Tolu Aina, Dáithí A. Stone, Peter A. Stott, Toru Nozawa, Arno G. J. Hilberts, Dag Lohmann, Myles R. Allen. Anthropogenic greenhouse gas contribution to flood risk in England and Wales in autumn 2000. Nature, Volume 470, 382–385 (17 February 2011).
-
-
-
-
-
-
-
Docking@home
-
- -
- T. Estrada, R. Armen, and M. Taufer: Automatic Selection of Near-Native Protein-Ligand Conformations using a Hierarchical Clustering and Volunteer Computing. In Proceedings of the International Conference On Bioinformatics and Computational Biology (ACM-BCB), August 2010, Niagara Falls, NY, USA.
-
-
-
-
-
-
-
-
- -
- Online Report on the S3 Analysis: http://einstein.phys.uwm.edu/FinalS3Results
-
- -
- Paper on the S4 analysis: Einstein@Home search for periodic gravitational waves in LIGO S4 data, by B. Abbott et al. (the LIGO Scientific Collaboration), Phys. Rev. D 79, 022001 (2009)
-
- -
- Paper on the early S5 analysis: Einstein@Home search for periodic gravitational waves in early S5 LIGO data. Abbott, B.P. et al. (the LIGO Scientific Collaboration) Phys. Rev. D 80, 042003 (2009).
-
- -
- Paper about the first radio pulsar discovery: Pulsar Discovery by Global Volunteer Computing. B. Knispel, B. Allen, J. M. Cordes, J. S. Deneva, D. Anderson et. al. Science 10 September 2010: Vol. 329. no. 5997, p. 1305
-
- -
- Paper about the second radio pulsar discovery: Arecibo PALFA Survey and Einstein@Home: Binary Pulsar Discovery by Volunteer Computing. B. Knispel, P. Lazarus, B. Allen, D. Anderson et. al. Astrophysical Journal Letters 732, p. L1, 2011.
-
-
-
-
-
-
-
-
- All publications with pdfs are available at http://multiscalelab.org/Publications
-
-
- -
- T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, in press J. Chem. Theory Comput. (2011).
-
- -
- I. Buch, S. K. Sadiq and G. De Fabritiis, Optimized potential of mean force calculations of standard binding free energy, in press J. Chem. Theory Comput. (2011)
-
- -
- Ignasi Buch, Toni Giorgino, and G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, PNAS 2011 ; published ahead of print June 6, 2011, doi:10.1073/pnas.1103547108
-
- -
- I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, and G. De Fabritiis. High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing. J. Chem. Inf. Model, March 2010.
-
- -
- J. Selent, F. Sanz, M. Pastor and G. De Fabritiis, Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors, PLOS Computational Biology, 6, e1000884 (2010) pdf.
-
- -
- K. Sadiq and G. De Fabritiis,Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing, Proteins 78, 2873 (2010) pdf.
-
- -
- G. Giupponi, M. Harvey and G. De Fabritiis, The impact of accelerator processors for high-throughput molecular modeling and simulation. Drug Discovery Today 13, 1052-8 (2008).
-
- -
- G. De Fabritiis, P. Coveney and J. Villa-Freixa, Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics. Proteins 73, 185-94 (2008).
-
- -
- M. Harvey, G. Giupponi, J. Villa-Freixa and G. De Fabritiis, PS3GRID.NET: Building a distributed supercomputer using the PlayStation 3. Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (2007).
-
- -
- PS3GRID.NET: A distributed computing environment for molecular simulations on the PlayStation 3. Presentation at the international symposium of biomedical informatics, 26-27 June Barcelona (2007).
-
- -
- G. De Fabritiis, Performance of the Cell processor for biomolecular simulations. Comp. Phys. Commun. 176, 660 (2007).
-
-
-
-
-
-
-
-
- -
- Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain. Molecular Cell 18, 687-98 (2005).
-
- -
- Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters 10:364-374 (2007).
-
- -
- Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A., Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T. B., Ramakrishnan, U., Reed, F. A. & Mountain, J. L. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Molecular Biology and Evolution 24:2180-2195 (2007).
-
- -
- Pettengill, J. B., & M. C. Neel. 2008. Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae). BMC Evolutionary Biology 8:264.
-
- -
- Regier, J. C., Zwick, A., Cummings, M. P., Kawahara, A. Y., Cho, S., Weller, S. J., Roe, A. D., Baixeras-Almela, J., Brown, J. W., Parr, C. S., Davis, D. R., Epstein, M. E., Hallwachs, W., Hausmann, A., Janzen, D. H., Kitching, I. J., Solis, M. A., Yen, S.-H., Bazinet, A., & Mitter, C. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evolutionary Biology 9:280 (2009).
-
- -
- Regier, J.C., Shultz, J. W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin J. W. & C.W. Cunningham C. W. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079-1083 (2010).
-
- -
- Reyna-Fabín, M., Laclette, J. P., Cummings, M. P., Sarma S. S. S., & García-Varela, M. Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome c oxidase. Hydrobiologia 644:361-370 (2010).
-
- -
- Regier, J.C., Zwick, A. Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods. PLoS ONE 6(8): e23408. doi:10.1371/journal.pone.0023408 (2011).
-
- -
- Zwick, A, Regier JC, Mitter C, Cummings MP. Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera). Syst Entomol. 36:31–43 (2011).
-
- -
- Kawahara, AY, Ohshima I, Kawakita A, Regier JC, Mitter C, Cummings MP, Davis DR, Wagner DL, De Prinis J, Lopez-Vaamonde C. Increased gene sampling provides ber support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evol Biol. 11:182 (2011).
-
- -
- Cho, S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S et al. Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)? Syst Biol. In press.
-
-
-
-
-
-
-
-
-
- -
- Penny MA, Maire N, Studer A, Schapira A, Smith TA. What Should Vaccine Developers Ask? Simulation of the Effectiveness of Malaria Vaccines. PLoS ONE 3(9): e3193. doi:10.1371/journal.pone.0003193 (2008)
-
- -
- Ross A, Penny M, Maire N, Studer A, Carneiro I, Schellenberg D, Greenwood B, Tanner M, Smith T. Modelling the Epidemiological Impact of Intermittent Preventive Treatment against Malaria in Infants. PLoS ONE 3(7): e2661 doi:10.1371/journal.pone.0002661. (2008)
-
- -
- Smith T, Maire N, Ross A, Penny M, Chitnis N, Schapira A, Studer A, Genton B, Lengeler C, Tediosi F, de Savigny D, Tanner M. Towards a comprehensive simulation model of malaria epidemiology and control. Parasitology (13):1507-16. (2008)
-
- -
- Gosoniu L, Vounatsou P, Sogoba N, Maire N, Smith T. Mapping malaria risk in West Africa using a Bayesian nonparametric non-stationary model. Computational Statistics and Data Analysis 53: 3358-3371. (2009)
-
- -
- Tediosi F, Maire N, Penny MA, Studer A, Smith TA. Simulation of the cost-effectiveness of malaria vaccines. Malaria Journal 8:127 doi:10.1186/1475-2875-8-127 (2009)
-
- -
- Chitnis N, Schapira A, Smith T, Steketee R. Comparing the effectiveness of malaria vector-control interventions through a mathematical model. Am J Trop Med Hyg. 83(2) (2010)
-
- -
- Ross A, Smith TA. Interpreting malaria age-prevalence and incidence curves: a simulation study of the effects of different types of heterogeneity. Malaria Journal 8:127 doi:10.1186/1475-2875-9-132 (2010)
-
- -
- Carneiro I, Smith L, Ross A, Roca-Feltrer A, Greenwood B, Schellenberg JA, Smith TA, Schellenberg D. Intermittent preventive treatment for malaria in infants: a decision-support tool for sub-Saharan Africa. Bulletin of the World Health Organization 2010;88:807-814. doi: 10.2471/BLT.09.072397 (2010)
-
- -
- Smith TA, Chitnis N, Briët OJ, Tanner M. Uses of mosquito-stage transmission-blocking vaccines against Plasmodium falciparum. Trends Parasitol. 2011 Jan 27. [Epub ahead of print]
-
- -
- Ross A, Maire N, Sicuri E, Smith T, Conteh L. Determinants of the Cost-Effectiveness of Intermittent Preventive Treatment for Malaria in Infants and Children. PLoS ONE 6(4): e18391. doi:10.1371/journal.pone.0018391 (2011)
-
- -
- Bretscher MT, Maire N, Chitnis N, Felger I, Owusu-Agyei S, Smith T. The distribution of Plasmodium falciparum infection durations. Epidemics 3, 109-118 (2011)
-
- -
- Maire N, Shilcutt SD, Walker DG, Tediosi F, Smith TA. Cost-Effectiveness of the Introduction of a Pre-Erythrocytic Malaria Vaccine into the Expanded Program on Immunization in Sub-Saharan Africa: Analysis of Uncertainties Using a Stochastic Individual-Based Simulation Model of Plasmodium falciparum Malaria. Value in Health 14:1028–1038 (2012)
-
- -
- Crowell V, Hardy D, Briet O, Chitnis N, Maire N, Smith T, Can we depend on case management to prevent re-establishment of P. falciparum malaria, after local interruption of transmission?. Epidemics 4, 1–8 (2012)
-
- -
- Smith T , Ross A , Maire N , Chitnis N , Studer A , et al. Ensemble Modeling of the Likely Public Health Impact of a Pre-Erythrocytic Malaria Vaccine. PLoS Med 9(1): e1001157. doi:10.1371/journal.pmed.1001157
-
- -
- Briet OJT, Hardy D, Smith TA Importance of factors determining the effective lifetime of a mass, long-lasting, insecticidal net distribution: a sensitivity analysis. Malaria Journal 11:20 doi:10.1186/1475-2875-11-20 (2012)
-
- -
- Brooks A, Briet OJT, Hardy D, Steketee R, Smith T. Simulated Impact of RTS,S/AS01 Vaccination Programs in the Context of Changing Malaria Transmission. PLoS ONE 7(3): e32587. doi:10.1371/journal.pone.0032587 (2012)
-
-
-
-
-
-
-
-
- -
- Travis Desell, David P. Anderson, Malik Magdon-Ismail, Heidi Newberg, Boleslaw Szymanski and Carlos A. Varela. An Analysis of Massively Distributed Evolutionary Algorithms. In the Proceedings of the 2010 IEEE Congress on Evolutionary Computation (IEEE CEC 2010), Barcelona, Spain, July 2010. To Appear.
-
- -
- Travis Desell, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos A. Varela, Heidi Newberg and David P. Anderson. Validating Evolutionary Algorithms on Volunteer Computing Grids. In the Proceedings of the 10th IFIP International Conference on Distributed Applications and Interoperable Systems (DAIS 2010), Amsterdam, Netherlands, June 2010. To Appear.
-
- -
- Nathan Cole, Travis Desell, Daniel Lombranaa Gonzalez, Francisco Fernandez de Vega, Malik Magdon-Ismail, Heidi Newberg, Boleslaw Szymanski and Carlos Varela. Evolutionary Algorithms on Volunteer Computing Platforms: The MilkyWay@Home Project. In F. Fernandez de Vega, E. Cantu-Paz (Eds.): Parallel and Distributed Computational Intelligence, SCI 269, pp 63-90. Springer-Verlag Berlin Heidelberg. 2010
-
- -
- Travis Desell. Asynchronous Global Optimization for Massive-Scale Computing. PhD thesis. Rensselaer Polytechnic Institute. 2009
-
- -
- Travis Desell, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos Varela, Heidi Newberg and Nathan Cole. Robust Asynchronous Optimization for Volunteer Computing Grids. In the 5th IEEE International Conference on e-Science (eScience2009), Oxford, UK, pages 263-270, December 2009.
-
- -
- Travis Desell, Anthony Waters, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos Varela, Matthew Newby, Heidi Newberg, Andreas Przystawik and Dave Anderson. Accelerating the MilkyWay@Home volunteer computing project with GPUs. In 8th International Conference on Parallel Processing and Applied Mathematics (PPAM 2009), Wroclaw, Poland, September 2009. To appear.
-
- -
- Nathan Cole. Maximum Likelihood Fitting of Tidal Streams with Application to the Sagittarius Dwarf Tidal Tails. PhD thesis. Rensselaer Polytechnic Institute. 2009.
-
- -
- Nathan Cole, Heidi Newberg, Malik Magdon-Ismail, Travis Desell, Kristopher Dawsey, Warren Hayashi, Jonathan Purnell, Boleslaw Szymanski, Carlos A. Varela, Benjamin Willett, and James Wisniewski. Maximum Likelihood Fitting of Tidal Streams with Application to the Sagittarius Dwarf Tidal Tails. Astrophysical Journal, 683:750-766, 2008.
-
- -
- Travis Desell, Boleslaw Szymanski, and Carlos A. Varela. An Asynchronous Hybrid Genetic-Simplex Search for Modeling the Milky Way Galaxy using Volunteer Computing. In Genetic and Evolutionary Computation Conference (GECCO 2008), Atlanta, Georgia, pages 921-928, July 2008.
-
- -
- Travis Desell, Boleslaw Szymanski, and Carlos A. Varela. Asynchronous Genetic Search for Scientific Modeling on Large-Scale Heterogeneous Environments. In Proceedings of the 17th International Heterogeneity in Computing Workshop (HCW/IPDPS'08), Miami, FL, pages 12pp, April 2008. IEEE.
-
- -
- Boleslaw Szymanski, Travis Desell, and Carlos A. Varela. The Effect of Heterogeneity on Asynchronous Panmictic Genetic Search. In Proc. of the Seventh International Conference on Parallel Processing and Applied Mathematics (PPAM'2007), LNCS, Gdansk, Poland, September 2007.
-
- -
- Travis Desell, Nathan Cole, Malik Magdon-Ismail, Heidi Newberg, Boleslaw Szymanski, and Carlos A. Varela. Distributed and Generic Maximum Likelihood Evaluation. In 3rd IEEE International Conference on e-Science and Grid Computing (eScience2007), Bangalore, India, pages 337-344, December 2007. Best paper finalist.
-
-
-
-
-
-
-
-
- -
- Meliciani I, Klenin K, Strunk T, Schmitz K, Wenzel W. (2009) Probing hot spots on protein-protein interfaces with all-atom free-energy simulation. J Chem Phys. 131, 034114.
-
-
-
-
-
-
-
-
Quake Catcher Network
-
- -
- Elizabeth S. Cochran, Jesse F. Lawrence, Carl Christensen, and Ravi S. Jakka. The Quake-Catcher Network: Citizen Science Expanding Seismic Horizons. Seismological Research Letters, Jan/Feb 2009.
-
-
-
-
-
-
-
-
- -
- Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ Jr, Burt A, Crisanti A. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature 12;473(7346):212-5 (2011).
-
- -
- Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 13;332(6031):816-21 (2011).
-
- -
- Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, T Montelione G, P Spiegel C, Liu DR, Baker D. A de novo protein binding pair by computational design and directed evolution. Mol Cell 42(2):250-60 (2011).
-
- -
- Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329(5989):309-13 (2010).
-
- -
- Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468(7325):790-5 (2010).
-
- -
- Srivatsan Raman, Oliver F. Lange, Paolo Rossi, Michael Tyka, Xu Wang, James Aramini, Gaohua Liu, Theresa A. Ramelot, Alexander Eletsky, Thomas Szyperski, Michael A. Kennedy, James Prestegard, Gaetano T. Montelione, David Baker. NMR Structure Determination for Larger Proteins Using Backbone-Only Data. Science 327, 1014-18 (2010).
-
- -
- Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. J. Biomol. NMR 43, 63-78 (2009).
-
- -
- Das R, Baker D. Prospects for de novo phasing with de novo protein models. Acta Crystallogr. D Biol. Crystallogr. 65, 169-75 (2009).
-
- -
- Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc. Natl. Acad. Sci. U.S.A. 106, 18978–83 (2009).
-
- -
- Kidd BA, Baker D, Thomas WE. Computation of conformational coupling in allosteric proteins. PLoS Comput. Biol. 5, e1000484 (2009).
-
- -
- Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A. Consistent blind protein structure generation from NMR chemical shift data. Proc. Natl. Acad. Sci. U.S.A. 105, 4685-90 (2008).
-
- -
- Rhiju Das, Madhuri Kudaravalli, Magdalena Jonikas, Alain Laederach, Robert Fong, Jason P. Schwans, David Baker, Joseph A. Piccirilli, Russ B. Altman, and Daniel Herschlag. Structural inference of native and partially folded RNA by high throughput contact mapping. Proc. Natl. Acad. Sci. U.S.A. 105, 4144-9 (2008).
-
- -
- Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-64 (2007).
-
- -
- Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J. Mol. Biol. 373, 503-19 (2007).
-
- -
- Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69 Suppl 8, 118-28 (2007).
-
- -
- Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 104, 14664-9 (2007).
-
- -
- Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. U.S.A. 103, 5361-6 (2006).
-
-
-
-
-
-
-
-
- -
- Posypkin, Mikhail and Semenov, Alexander and Zaikin, Oleg (2012) Using BOINC desktop grid to solve large scale SAT problems. Computer Science, 13 (1). pp. 25-34. ISSN 1508-2806
-
-
-
-
-
-
-
-
- -
- David P. Anderson, Jeff Cobb, Eric Korpela, Matt Lebofsky, Dan Werthimer. SETI@home: An Experiment in Public-Resource Computing. Communications of the ACM, Vol. 45 No. 11, November 2002, pp. 56-61.
-
-
-
-
-
-
-
SIMAP
-
- -
- Rattei T, Tischler P, Arnold R, Hamberger F, Krebs J, Krumsiek J, Wachinger B, Stümpflen V, Mewes W. SIMAP--structuring the network of protein similarities. Nucleic Acids Res. 2008 Jan;36(Database issue):D289-92. Epub 2007 Nov 23.
-
- -
- Rattei T, Arnold R, Tischler P, Lindner D, Stümpflen V, Mewes HW. SIMAP: the similarity matrix of proteins. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D252-6.
-
- -
- Arnold R, Rattei T, Tischler P, Truong MD, Stümpflen V, Mewes W. SIMAP--the similarity matrix of proteins. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii42-6.
-
-
-
-
-
-
-
Spinhenge@home
-
- -
- Christian Schröder, Ruslan Prozorov, Paul Kögerler, Matthew D. Vannette, Xikui Fang, Marshall Luban, Akira Matsuo, Koichi Kindo, Achim Müller, Ana Maria Todea, Multiple nearest-neighbor exchange model for the frustrated Keplerate magnetic molecules Mo72Fe30 and Mo72Cr30. submitted to Phys. Rev. B (2008), arXiv.org e-Print archiv, Jan 2008
-
-
-
-
-
-
-
-
Virtual Prairie
-
- -
- C. Monya, M. Garbeyb, M. Smaouib, M.-L. Benota. Large scale parameter study of an individual-based model of clonal plant with volunteer computing. Ecological Modelling 222 (2011) 935–946.
-
-
-
-
-
-
-
-
-
- The Clean Energy Project
-
-
- -
- Roberto Olivares-Amaya, Carlos Amador-Bedolla, Johannes Hachmann, Sule Atahan-Evrenk, Roel S. Sánchez-Carrera, Leslie Vogt and Alán Aspuru-Guzik Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics Energy & Environmental Science, 2011, 4, 4849-4861 doi:10.1039/C1EE02056K
-
- -
- Johannes Hachmann, Roberto Olivares-Amaya, Sule Atahan-Evrenk, Carlos Amador-Bedolla, Alan Aspuru-Guzik,The Harvard Clean Energy Project. Large-scale computational screening and design of molecular motifs for organic photovoltaics on the World Community Grid American Physical Society, APS March Meeting 2011, March 21-25, 2011, abstract #J28.004
-
- -
- Sokolov, A.N. et al. From computational discovery to experimental characterization of a high hole mobility organic crystal. Nat. Commun. 2:437 doi: 10.1038/ncomms1451 (2011).
-
-
-
-
- Computing for Clean Water
-
-
-
-
- Discovering Dengue Drugs - Together
-
-
-
-
- FightAIDS@Home
-
-
- -
- Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ. Virtual Screening with AutoDock: Theory and Practice. Expert Opin Drug Discov. 2010 Jun 1;5(6):597-607
-
- -
- Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. A dynamic model of HIV integrase inhibition and drug resistance J Mol Biol. 2010 Mar 26;397(2):600-15. Epub 2010 Jan 22.
-
- -
- Perryman, A. L., Zhang, Q., Soutter, H. H., Rosenfeld, R., McRee, D. E., Olson, A. J., Elder, J. E. and David Stout, C. (2010), Fragment-Based Screen against HIV Protease. Chemical Biology & Drug Design, 75: 257–268. doi: 10.1111/j.1747-0285.2009.00943.x
-
- -
- Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009 Dec;30(16):2785-91.
-
- -
- Max W. Chang, William Lindstrom, Arthur J. Olson, and Richard K. Belew . Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries. J. Chem. Inf. Model., 47 (3), 1258 -1262, 2007.
-
-
-
-
- Help Conquer Cancer
-
-
- -
- Yulia Kotseruba, Christian A Cumbaa1 and Igor Jurisica, High-throughput protein crystallization on the World Community Grid and the GPU 2012 Journal of Physics: Conference Series 341 012027 doi:10.1088/1742-6596/341/1/012027
-
- -
- Christian A. Cumbaa, Igor Jurisica, Protein crystallization analysis on the World Community Grid J Struct Funct Genomics (2010) 11:61–69 doi:10.1007/s10969-009-9076-9
-
- -
- Edward H. Snell, Angela M. Lauricella, Stephen A. Potter, Joseph R. Luft, Stacey M. Gulde, Robert J. Collins, Geoff Franks, Michael G. Malkowski, Christian Cumbaa, Igor Jurisica, and George T. DeTitta Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples Acta Crystallogr D Biol Crystallogr. 2008 November 1; 64(Pt 11): 1131–1137. doi:10.1107/S0907444908028059
-
- -
- Edward H. Snell,ab* Joseph R. Luft,ab Stephen A. Potter,a Angela M. Lauricella,a Stacey M. Gulde,a Michael G. Malkowski,ab Mary Koszelak-Rosenblum,a Meriem I. Said,a Jennifer L. Smith,a Christina K. Veatch,a Robert J. Collins,a Geoff Franks,a Max Thayer,a Christian Cumbaa,c Igor Jurisica,c and George T. DeTittaab Establishing a training set through the visual analysis of crystallization trials. Part I: ∼150 000 images Acta Crystallogr D Biol Crystallogr. 2008 November 1; 64(Pt 11): 1123–1130. doi:10.1107/S0907444908028047
-
- -
- C.A. Cumbaa & I. Jurisica, Scale Changes Everything – Crystallography Image Analysis on the World Community Grid. 22nd High Performance Computing Symposium - Québec City, CA. June, 2008
-
-
-
-
- Help Cure Muscular Dystrophy
-
-
- -
- Stefan Engelen Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, and Alessandra Carbone. Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling PLoS Comput Biol. 2009 January; 5(1): e1000267. doi:10.1371/journal.pcbi.1000267
-
- -
- Sophie Sacquin-Mora1, Alessandra Carbone, and Richard Lavery. Identification of Protein Interaction Partners and Protein–Protein Interaction Sites Journal of Molecular Biology, 2008 Aug 7.
-
- -
- V. Bertsis, R. Bolze, F. Desprez, K. Reed. Large Scale Execution of a Bioinformatic Application on a Volunteer Grid. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC), In conjunction with IPDPS 2008, Miami, Florida, April, 2008.
-
- -
- Viktors Bertis, Raphaël Bolze, Frédéric Desprez and Kevin Reed. From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application Journal of Grid Computing Volume 7, Number 4, 463-478, DOI: 10.1007/s10723-009-9130-7
-
-
-
-
- Help Defeat Cancer
-
-
- -
- Foran DJ, Yang L, Chen W, Hu J, Goodell LA, Reiss M, Wang F, Kurc T, Pan T, Sharma A, Saltz JH. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology. J Am Med Inform Assoc. 2011 Jul-Aug;18(4):403-15. Epub 2011 May 23.
-
- -
- Patrick Widener, Wenjin Chen, Fusheng Wang, Lin Yang, Jun Hu, Vicky Chu, Joel H. Saltz, David J. Foran, and Tahsin Kurc. Grid-Enabled, High-performance Microscopy Image Analysis. The 2nd International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making. Bejing, China. HP-MICCAI 2010 International Workshop. Pages 70-79, 2010.
-
- -
- Yang L, Chen W, Meer P, Salaru G, Goodell LA, Berstis V, Foran DJ. Virtual microscopy and grid-enabled decision support for large-scale analysis of imaged pathology specimens IEEE Trans Inf Technol Biomed. 2009 Jul;13(4):636-44. Epub 2009 Apr 14.
-
- -
- Yang L, Tuzel O, Chen W, Meer P, Salaru G, Goodell LA, Foran DJ. PathMiner: a Web-based tool for computer-assisted diagnostics in pathology. IEEE Trans Inf Technol Biomed. 2009 May;13(3):291-9. Epub 2009 Jan 20.
-
- -
- Lin Yang, Wenjin Chen, Peter Meer1, Gratian Salaru, Michael D. Feldman, and David J. Foran High Throughput Analysis of Breast Cancer Specimens on the Grid. Proceedings on Medical Image Computing and Computer-Assisted Intervention. (MICCAI) Brisbane, Australia. October, 2007.
-
-
-
-
- Human Proteome Folding
-
-
- -
- Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armb J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: Proteome-scale prediction of structure and function Genome Res. 2011 Nov;21(11):1981-94. Epub 2011 Aug 8.
-
- -
- Boxem, Mike; Maliga, Zoltan; Klitgord, Niels; Li, Na; Lemmens, Irma; Mana, Miyeko; de Lichtervelde, Lorenzo; Mul, Joram D.; van de Peut, Diederik; Devos, Maxime; Simonis, Nicolas; Yildirim, Muhammed A.; Cokol, Murat; Kao, Huey-Ling; de Smet, Anne-Sophie; Wang, Haidong; Schlaitz, Anne-Lore; Hao, Tong; Milstein, Stuart; Fan, Changyu; Tipsword, Mike; Drew, Kevin; Galli, Matilde; Rhrissorrakrai, Kahn; Drechsel, David; Koller, Daphne; Roth, Frederick P.; Iakoucheva, Lilia M.; Dunker, A. Keith; Bonneau, Richard; Gunsalus, Kristin C.; Hill, David E.; Piano, Fabio; Tavernier, Jan; van den Heuvel, Sander; Hyman, Anthony A.; Vidal, Marc A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis Cell doi:10.1016/j.cell.2008.07.009 (volume 134 issue 3 pp.534 - 545)
-
- -
- Bonneau, Richard; Facciotti, Marc T.; Reiss, David J.; Schmid, Amy K.; Pan, Min; Kaur, Amardeep; Thorsson, Vesteinn; Shannon, Paul; Johnson, Michael H.; Bare, J. Christopher; Longabaugh, William; Vuthoori, Madhavi; Whitehead, Kenia; Madar, Aviv; Suzuki, Lena; Mori, Tetsuya; Chang, Dong-Eun; DiRuggiero, Jocelyne; Johnson, Carl H.; Hood, Leroy; Baliga, Nitin S. A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell Cell doi:10.1016/j.cell.2007.10.053 (volume 131 issue 7 pp.1354 - 1365)
-
- -
- Lars Malmström, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau, David Baker. Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol 5(4).
-
-
-
-
- Genome Comparison
-
-
- -
- Thomas Dan Otto, Marcos Catanho, Cristian Tristão, Márcia Bezerra, Renan Mathias Fernandes, Guilherme Steinberger Elias, Alexandre Capeletto Scaglia, Bill Bovermann, Viktors Berstis, Sergio Lifschitz, Antonio Basílio de Miranda and Wim Degrave ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes Bioinformatics (2010) 26 (5): 705-707. doi: 10.1093/bioinformatics/btq011
-
-
-
-
- Nutritious Rice for the World
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/source/Guides/3rdpartyapps.htm.erb b/source/Guides/3rdpartyapps.htm.erb
deleted file mode 100644
index e6683c35..00000000
--- a/source/Guides/3rdpartyapps.htm.erb
+++ /dev/null
@@ -1,298 +0,0 @@
----
-title: "Gridcoin - 3rd Party Applications"
-description: "A list of 3rd party BOINC applications - use at your own discretion!"
----
-
-
-
-
-
-
BOINC 3rd party apps
-
-
-
-
-
-
-
-
-
-
-
-
-
These applications are not endorsed by BOINC or Gridcoin, use them at your own risk.
-
We do not provide instructions for installing or using these applications.
-
-
-
Windows
-
-
-
- Add-on |
- Description |
-
-
-
-
- SETI@BOINCWatch |
- A SETI@Home/BOINC client watcher! User statistics powered by BOINCStats |
-
-
- SQL Setup for BoincSpy |
- Stores Workunits into SQL database |
-
-
- CPDNSpy |
- Stats/Benchmarkprogram. Only for CPDN!!! |
-
-
- ThreadMaster |
- Control max CPU usage and prevent overheating (not specific to BOINC) |
-
-
- SETISpirit |
- SETIspirit is free add-on tool for SETI@home users which provides information about the tasks, the SETI@home project status, workunits and credits, statistic charts and a detailed sky map. |
-
-
- BOINCcalculator |
- Show details of CPDN jobs |
-
-
- SETI@home-MapView |
- SETI@home-Mapview creates skymaps for the BOINC projects SETI@home-II, Einstein@home and Astropulse. |
-
-
- BoincLogX |
- BoincLogX creates detailed logfiles for all BOINC projects. |
-
-
- BoincSpy |
- Views BOINC project statistics |
-
-
- TThrottle |
- TThrottle throttles CPU usage to keep its temperature below a limit you select. |
-
-
- BOINC Client Configuration |
- Windows GUI for editing the client configuration file |
-
-
- BoincTasks |
- An advanced and powerful BOINC GUI |
-
-
- BoincView |
- Advanced BOINC manager for networks |
-
-
- SETI@BOINCWatch(.NET 2.0) |
- A SETI@Home/BOINC client watcher! User statistics powered by BOINCStats. But now built with the .NET environment. |
-
-
- SETI@BOINCWatch(.NET) |
- A SETI@Home/BOINC client watcher! User statistics powered by BOINCStats. But now built with the .NET environment. |
-
-
-
-
-
Linux
-
-
-
- Add-on |
- Description |
-
-
-
-
- boincctl |
- Script to start boinc at boot time. |
-
-
- SETI@Boinc Tracker |
- SETI@Boinc Tracker is a GUI Client for Tracking Boinc CLI Client! |
-
-
- boinctui |
- Fullscreen text mode manager for BOINC |
-
-
- boinctop |
- top like view of boinc status |
-
-
- CPU limiter |
- Limits the CPU usage (good for laptops) |
-
-
- MultiTail |
- Multitail shows several simultaneous tails in different curses windows. |
-
-
- BOINC Monitor |
- Plasmoid to show BOINC status on the KDE desktop |
-
-
- BOINCTail |
- BOINCTail displays the status of jobs running in the BOINC environment in a 'tail-like' way. |
-
-
- Boinc bash script |
- Boinc state displayer |
-
-
- BOINCprog |
- A BOINC project progress monitor |
-
-
- rc.boinc (Slackware) |
- rc.boinc - Slackware Startup Script |
-
-
- boinc-suse |
- Init script for SuSE 9.2 and 9.3 |
-
-
- Boinctray |
- A system tray application for monitoring the BOINC client |
-
-
- KBoingMgr |
- A Linux/KDE replacement for the standard BOINC Manager |
-
-
- BOINCSTAT |
- Command line view of BOINC status |
-
-
-
-
-
Mac
-
-
-
Mobile
-
-
-
- Add-on |
- Description |
-
-
-
-
- BoincTasks Mobile |
- BOINC graphical interface for mobile devices (Android, iPhone, iPad) |
-
-
-
- AndroBOINC |
- BOINC graphical interface for Android devices |
-
-
-
-
-
Web browser toolbars and plugins
-
-
-
- Add-on |
- Description |
-
-
-
-
- SAH User Statistics |
-
- An extension for Firefox (works only with 1.0 to 1.5;
- may work under Mozilla)
- that displays your stats for SAH
- |
-
-
- BOINC Server Status |
- Yahoo! widget adds the BOINC Online Scheduler image to your desktop. |
-
-
-
-
-
Web applications
-
-
-
- Add-on |
- Description |
-
-
-
-
- Progress Thru Processors |
- Facebook-based interface to BOINC |
-
-
-
- GOINC |
- GOINC: A Google homepage module for keeping tabs on BOINC. |
-
-
-
- BOINC Milestones |
- Facebook application that posts credit milestones in your Status |
-
-
-
- Forum signature showing jobs in progress |
- A PHP script that generates a forum signature showing jobs in progress |
-
-
-
- BoincPHP5-GUI |
- Monitor and control Boinc from a web browser |
-
-
-
- SETI@home/BOINC progress status |
- Show your SETI@home/BOINC progress on your homepage |
-
-
-
- Boinc LCS |
- Shows the current state and other information from an unlimited number of BOINC clients connected to the Internet. |
-
-
-
-
-
-
-
-
-
diff --git a/source/Guides/security.htm.erb b/source/Guides/security.htm.erb
index 65998fdb..e5f5d1d8 100644
--- a/source/Guides/security.htm.erb
+++ b/source/Guides/security.htm.erb
@@ -13,80 +13,12 @@ description: "A brief security guide for Gridcoin users."
Wallet security recommendations:
- - Create a paper wallet and store it in a waterproof, safe environment.
- - Backup the wallet.dat and gridcoinresearch.conf files on encrypted USB sticks and store them somewhere safe.
- - Alternatively, store an encrypted zip/rar/tar on any form of storage medium and keep it safe.
- - Regularly check that your backups work - if you encrypt your wallet then forget the pass, you're in trouble..
+ - For long term storage, consider creating a paper wallet and store it in a waterproof, safe environment.
+ - Regularly backup the wallet.dat and gridcoinresearch.conf files and store them somewhere safe. Verify your backup system works.
+ - Encrypt your Gridcoin wallet within the client, don't lose the password.
- Read this wallet security guide (for Bitcoin, but relevant to Gridcoin to some degree).
-
-
Securing your browser
-
- One of the most common attack vectors is through your web browser, so take precautionary measures to minimize risk of loss of funds/exposure to malware.
-
-
Non-exhaustive browser security recommendation:
-
- - Stop using Internet Explorer! Switch to Firefox, Chrome, or one of the many variants of the two.
- - Do not use the same password for multiple sites. NEVER re-use a password!
- - Use long passwords! the longer, the more difficult to crack.
- - Consider a password manager such as KeePassXC to create and store long/unique passwords.
- - Use 2 factor authentication like a Yubikey, or GoogleAuth on any website that offers it; it's a second layer of defence against phishing.
- - If you've been sent a shortened link, either use a link preview service or do not click it!
- - Disable any extensions that have been installed by 3rd party software - java/toolbars/etc, minus antivirus.
- - Keep plugins up-to-date (flash/java/etc).
- - Use StartPage instead of Google.
-
-
-
Browser extension recommendations for extra security:
-
- - uBlock Origin: Eliminate adverts from the internet; adverts often are malicious! Both "AdBlock" extensions, Plus and Edge, are now considered out-of-date.
- - NoScript: Nerfs scripts on the internet; you have to manually allow sites to run scripts. Can help prevent malicious scripts running.
- - Policeman: Alternative to NoScript. Nerfs scripts on the internet.
- - HTTPS Everywhere: An extension made by the EFF; Enforces an https (SSL) connection on sites whenever possible.
- - requestpolicy: Protects against CSRF (Controls cross-site requests).
- - Cookie Controller: Manage site cookie permissions (browse & remove cookies).
- - https-finder: Detects valid https pages as you browse.
- - RefControl: Hides/forges your referers.
- - Lastpass: Another secure password manager. Combine with a Yubikey and you'll have incredibly secure authentication online! Highly recommended!
- - Random Agent Spoofer: Adding all these extensions makes your browser stick out like a sore thumb! Spoof your fingerprints!
- - Decentraleyes: Local CDN Emulation
-
-
-
-
Securing your communications
-
- It's crucial that your private communications online are not intercepted by any malicious entity; privacy is a human right, take yours back!
-
-
- - Do not use skype!
- - Use a VPN to evade censorship, MITM attacks & totalitarian governments. Find the best vpn for you.
- - Encrypt your private emails using PGP.
- - Always attempt to use multi-party encryption if performing group chat/conferences. At the very least, password protect chat rooms.
- - Use OTR for 1-1 secure communications (Pidgin + OTR), keep an eye out for multi-party OTR in the future.
- - Don't share ANY of your personal information online. Use aliases.
- - Use encrypted texting apps e.g. Chatsecure
- - Keep usage of social media to a minimum; if you're not paying for the service, you're the product being sold.
- - Do not use an email provider based in USA, instead use a secure alternative (link to list).
-
-
-
-
Securing your computer
-
- Most of these tips are a given, but it's good to remember that they are quite important to adhere to at all times.
-
-
- - Use Secunia PSI to keep software constantly up to date.
- - Keep your operating system up to date (Windows updates/Ubuntu apt-get upgrade/Fedora yum -y upgrade/etc) & dont run a cracked version of your operating system (Good way to infect your PC & be a victim of ID theft).
- - Keep usage of cracked/pirated software/games to an absolute minimum; keygens and pirate software can be (usually are) a source of malware.
- - If you must install insecure software, run it in a sandbox!
- - Install an antivirus program (Bitdefender paid versions are good!). Scan all files that you download from the internet, especially from forums & P2P sites/apps.
- - Keep offline backups of your important data.
- - Install theft prevention software on mobile devices, examples are: Prey, Lojack, etc.
- - Encrypt your devices' storage, especially if you've got a mobile wallet.
- - Do not share any of your account credentials to anyone, don't write them down, and don't store them insecurely on your PC.
-
-
diff --git a/source/Guides/whitelist.htm.erb b/source/Guides/whitelist.htm.erb
index 4f29f105..a8dfbd82 100644
--- a/source/Guides/whitelist.htm.erb
+++ b/source/Guides/whitelist.htm.erb
@@ -10,7 +10,7 @@ description: "The Gridcoin whitelist is a list of community-approved BOINC proje
Whitelist justification
The whitelist was created to increase security and to focus user's resources on active projects.
-
+
Discussion
CCT Whitelist thread
Projects subforum
@@ -32,7 +32,7 @@ description: "The Gridcoin whitelist is a list of community-approved BOINC proje
Greylist
When projects are running out of work or are offline for temporary maintenance they are placed on the Greylist. These projects will not reward Gridcoin until they meet the requirements to be placed back on the whitelist again. Please see various social media (Twitter, Facebook, Reddit, Slack) for notices about greylisted projects.
-
Please see The official Greylist website for daily updates on which projects are added and removed from the Greylist.
+
Please see This Gridcoin greylist monitoring website for daily updates on which projects are added and removed from the Greylist.
This document outlines the Greylist procedure for all whitelisted projects.
@@ -85,23 +85,23 @@ description: "The Gridcoin whitelist is a list of community-approved BOINC proje
<% if project.cpu == "yes" %>
-
- <% else %>
-
+ ✔️
+ <% else %>
+ ❌
<% end %>
|
<% if project.gpu == "yes" %>
-
- <% else %>
-
- <% end %>
+ ✔️
+ <% else %>
+ ❌
+ <% end %>
|
-
+ 📊
|
-
+ 📈
|
<% end %>
@@ -138,17 +138,17 @@ description: "The Gridcoin whitelist is a list of community-approved BOINC proje
<% if project.cpu == "yes" %>
-
- <% else %>
-
+ ✔️
+ <% else %>
+ ❌
<% end %>
|
<% if project.gpu == "yes" %>
-
- <% else %>
-
- <% end %>
+ ✔️
+ <% else %>
+ ❌
+ <% end %>
|
<% end %>
diff --git a/source/assets/css/index_hotfixes.css b/source/assets/css/index_hotfixes.css
new file mode 100644
index 00000000..72f521c1
--- /dev/null
+++ b/source/assets/css/index_hotfixes.css
@@ -0,0 +1,12 @@
+div.dropdown a {
+ text-decoration:none;
+}
+
+div.dropdown a.dropdown-header {
+ color:black !important;
+}
+
+div.footer_placeholder a {
+ text-decoration:none;
+ font-weight:normal;
+}
diff --git a/source/assets/css/table.css b/source/assets/css/table.css
index 2a690792..1211fb1c 100644
--- a/source/assets/css/table.css
+++ b/source/assets/css/table.css
@@ -21,4 +21,4 @@ td a:hover {
th {
color: #FFFFFF;
border-bottom-color: #434343 !important;
-}
\ No newline at end of file
+}
diff --git a/source/assets/img/Exchanges/bitker.png b/source/assets/img/Exchanges/bitker.png
new file mode 100644
index 00000000..a6a4517f
Binary files /dev/null and b/source/assets/img/Exchanges/bitker.png differ
diff --git a/source/contact.htm.erb b/source/contact.htm.erb
index 679c26f4..5461ae70 100644
--- a/source/contact.htm.erb
+++ b/source/contact.htm.erb
@@ -11,7 +11,7 @@ description: "How to get in contact with the Gridcoin developers and community."
How to get in contact with us!
-
The Gridcoin community as of mid August has approximately 12k registered users in team Gridcoin, with approx 3k actively crunching. These users are spread across many platforms such as:
+
Our large userbase is spread the following chat platforms: