Abstract
In this paper, we state our aims and aspirations for building a global network of likeminded people interested in developing and encouraging students in the field of computational biophysics (CB). Global capacity building efforts have uncovered local computational talent in virtually every community regardless of where the students reside. Our vision is to discover and encourage these aspiring investigators by suggesting ways that they and other "garage scientists" can participate in new science even if they have no access to sophisticated research infrastructure. We argue that participatory computing in the "cloud" is particularly suitable for CB and available to any budding computational biophysicist if he or she is provided with open-minded mentors who have the necessary skills and generosity. We recognize that there are barriers to the development of such remote collaborations, and we discuss possible pathways to overcome these barriers. We point out that this Special Issue of Biophysical Reviews provides a much-needed forum for the development of several specific applications of CB.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
AmazonWeb Services (2012) Amazon Elastic Compute Cloud. http://aws.amazon.com/ec2
Anisimov VM, Cavasotto CN (2011) Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain. J Comp Chem 32:2254–2263
Astronomical Society of the Pacific (2012) Past Amateur Achievement Award winners. http://www.astrosociety.org/membership/awards/pastamateur.html
MIT BioEECS (2012) Computational Biophysics. http://www.eecs.mit.edu/bioeecs/CompBioPhy.html
Brabham DC (2012) The myth of amateur crowds: a critical discourse analysis of crowdsourcing coverage. Inform Comm Soc 15:394–410
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, The 1000 Genomes Project Consortium (2012) The 1000 Genomes Project: data management and community access. Nat Meth 9:459–462
Cook G (2011) How crowdsourcing is changing science. The Boston Globe, Boston. (November 11 issue)
Craddock TJA, Tuszynski JA, Chopra D, Casey N, Goldstein LE, Hameroff SR, Tanzi RE (2012) The zinc dyshomeostasis hypothesis of Alzheimer’s disease. PLoS One 7:e33552
Google (2012) Google Code. http://code.google.com
Khatib F, DiMaio F, Foldit Contenders Group, Foldit Void Crushers Group, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popovic Z, Jaskolski M, Baker D (2011) Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol 18:1175–1177
LAFeBS (2012) Latin American Federation of Biophysical Societies. http://www.lafebs.org
Ledford H (2010) Garage biotech: life hackers. Nature 467:650–652
X.-L. Lu (2012) 3DNA: a suite of software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. http://x3dna.org/
Lu X-J, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108–5121
Lu X-J, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures. Nat Protoc 3:1213–1227
MentorNet (2012) e-Mentoring for diversity in engineering and science. http://www.mentornet.net
Morales MM, dos Remedios CG (2011) Biophysical educational experiment: science and goodwill in Latin America and Africa. Biophys Rev 3:101–106
National Center for Biotechnology Information (2012) Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781–1802
L. B. Poole (2011) Structural and computational biophysics training program. NIH research portfolio online reporting tools. http://report.nih.gov/ Project number 1T32GM095440-01
Qin Z, Kreplak L, Buehler MJ (2009) Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments. PLoS One 4:e7294
Rusu M, Wriggers W (2012) Evolutionary bidirectional expansion for the annotation of alpha helices in cryo-electron microscopy reconstructions. J Struct Biol 177:410–419
Rusu M, Starosolski Z, Wahle M, Rigort A, Wriggers W (2012) Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs. J Struct Biol 178:121–128
Sagot M-F, McKay BJM, Myers G (2009) ISMB/ECCB 2009 Stockholm. Bioinformatics 25:1570–1573
GNU Savannah (2012) Concurrent Versions System. http://savannah.nongnu.org/projects/cvs
Starosolski Z, Szczepanski M, Wahle M, Rusu M, Wriggers W (2012) Developing a denoising filter for electron microscopy and tomography data in the cloud. Biophys Rev doi:10.1007/s12551-012-0083-x
Swiss Institute of Bioinformatics (2012) SIB Bioinformatics Resource Portal. http://www.expasy.org
Tranche Developers Group (2012) Tranche Project file storage and dissemination software. https://trancheproject.org
Wang JTL, Wu CH, Wang PP (2003) Computational Biology and Genome Informatics. World Scientific, Singapore
Acknowledgments
We thank Mirabela Rusu for creating Fig 1 and for discussions. We are also grateful for discussions with Zbigniew Starosolski and Manuel Wahle. This work was funded in part by the National Institutes of Health (research grants R01GM62968 to W.W. and R01GM34809 to W.K.O.).
Conflict of interest
None
Author information
Authors and Affiliations
Corresponding author
Additional information
Special Issue: Computational Biophysics
Rights and permissions
About this article
Cite this article
Wriggers, W., Olson, W.K. & dos Remedios, C.G. Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing. Biophys Rev 4, 153–160 (2012). https://doi.org/10.1007/s12551-012-0085-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12551-012-0085-8