Herbert J. Bernstein

	Contact Information	Professor of Computer Science Department of Mathematics and Computer Science Div. of Nat. Sci. and Math. Brookhaven Campus B205/A210 Dowling College 1300 William Floyd Parkway. Shirley, NY 11967 +1-631-244-1935
	Research Interests	bioinformatics, data representation, molecular graphics, laboratory automation, numerical linear algebra, networking and data communications, software engineering

Teaching

At Dowling College, Oakdale, NY

• Fall 2013: CSC 2025A -- Data Structures (online course),
  CSC 2060N -- Computer Organization (online course),
  MTH 1007A -- Operations Research (online course),
  MTH 1014A -- Pre-Calculus (online course)
• Spring 2013: CSC 2281A -- Network Design & Queuing Theory (online course),
  CSC 3072A -- Database Systems (online course),
  CSC 3971N -- Advanced Programming I (online course),
  CSC 3982N -- Advanced Software Engineering II (online course),
  MTH 1014A -- Pre-Calculus (online course)
• Fall 2012: CSC1009N -- Introduction to Spreadsheets and Data Analysis (online course),
  CSC 2060N -- Computer Organization (online course),
  CSC 3981N -- Advanced Software Engineering I (online course),
  MTH 1002A -- Fundamentals of Mathematics (online course),
  
• Spring 2012: CSC 1023N -- Introduction to Computer Science (online course),
  CSC 2281A -- Network Design and Queuing Theory (online course),
  CSC 3080A -- Operating Systems (online course),
  MTH 1007A -- Operations Research (online course)
• Fall 2011: CSC 1024N -- Introduction to Programming,
  CSC 3171A -- Algorithms,
  CSC 3971N -- Advanced Programming
• Spring 2011: CSC 1023N -- Introduction to Computer Science,
  CSC 2025A -- Data Structures,
  CSC 2281A -- Network Design & Queuing Theory
• Fall 2010: MTH 1002A -- Fundamentals of Mathematics,
  CSC 1023N -- Introduction to Computer Science,
  CSC 2060N Computer Organization
• Fall 2009 -- Spring 2010: on Sabbatical
• Spring 2009: MTH 1007A -- Operations Research,
  CSC 3149A -- Compilers,
  CSC 1009N -- Introduction to Spreadsheets and Visual Basic
• Fall 2008: NSM 6600 -- Technologies for Research and Instruction,
  MTH 1002 -- Fundamentals of Mathematics (2 sections)
• Spring 2008: CSC 3962 -- Project-Oriented Computer Science
  CSC 4962 -- Project-Oriented Computer Science Research,
  CSC 1009 -- Introduction to Spreadsheets and Visual Basic
• Fall 2007: Technologies for Research and Teaching,
  CSC 3961 -- Project-Oriented Computer Science
  CSC 4961 -- Project-Oriented Computer Science Research
• Spring 2007: CSC 3171 -- Algorithms,
  CSC 3962N -- Project-Oriented Computer Science,
  CSC 4962N -- Project-Oriented Computer Science Research
• Fall 2006: NSM 6600 -- Technologies for Research and Instruction,
  CSC 3961N -- Project-Oriented Computer Science
  CSC 4961N -- Project-Oriented Computer Science Research
• Spring 2006: MTH 1002A -- Fundamentals of Mathematics,
  CSC 4181N -- Project-Oriented Computer Science I
  CSC 4182N -- Project-Oriented Computer Science II
• Fall 2005: NSM 6600 -- Technologies for Research and Instruction,
  CSC 4181N -- Project-Oriented Computer Science I
  CSC 4182N -- Project-Oriented Computer Science II
• Spring 2005: CSC 3080 -- Operating Systems,
  CSC 4175 -- Software Engineering
  CSC 4177 -- Senior Project,
  MTH 1002 -- Fundamentals of Mathematics
• Fall 2004: CSC 1012 -- Introduction to Computer Science,
  NSM 6600 -- Technology in Research and Instruction,
  NSM 6602 -- Experiment Design
• Spring 2004: CSC 1012 -- Introduction to Computer Science,
  CSC 1071 -- Data Structures
• Fall 2003: CSC 1012 -- Introduction to Computer Science,
  CSC 1071 -- Data Structures
• Spring 2003: CSC 080 -- Operating Systems,
  MTH 002 -- Fundamentals of Mathematics,
  MTH 014 -- Pre-Calculus
• Fall 2002: CSC 181 -- Advanced Research Topics in Computer Science,
  CSC 077 -- Intermediate Java Programming,
  CSC 175/177 -- Software Engineering/Senior Project

Research-Related Web Sites

• Search of Alterate Unit Cells
• New and Upgraded CIF Software
• Management of Experimental Data in Structural Biology
• Structural Biology Extensible Visualization Scripting Language
• Accessible Retired Computers in Biology (ARCiB) Project
• PDF of "To transpose or not to transpose; that is the question -- performance issues in the use of Java-based XML software for real-world problems," Design and Analysis Seminar, 26 Sep 2001
• http://www.bernstein-plus-sons.com/software/xmlCIF/: a site discussing work on conversion between XML and CIF.
• http://www.bernstein-plus-sons.com/software/CBF: CBF - specifications and an ANSI-C API for CBF/imgCIF
• http://www.bernstein-plus-sons.com/software/DISCUSS.fortapps.html: a discussion on converting Fortran applications to mmCIF
• http://www.bernstein-plus-sons.com/software/rasmol: rasmol - a version of R. Sayle's RasMol which accepts core CIF and mmCIF datasets and which can display alternate conformers and multiple NMR models
• http://www.openrasmol.org OpenRasMol web site
• http://www.bernstein-plus-sons.com/software/ciftbx: CIFtbx - a CIF toolbox (with Cyclops and cif2cif)
• http://www.bernstein-plus-sons.com/software/cif2pdb: cif2pdb - a program to convert mmCIF to pseudo-PDB format
• http://www.bernstein-plus-sons.com/software/pdb2cif: pdb2cif - a script to convert from PDB format to mmCIF

Education

• Ph.D. 1968, Mathematics, New York University, Graduate School of Arts and Sciences.
• M.S. 1965, Mathematics, New York University, Graduate School of Arts and Sciences.
• B.A., magna cum laude with honors in mathematics, 1964, New York University, Washington Square College of Arts and Science.

Professional Societies

• Mathematical Association of America (Life Member)
• American Mathematical Society
• Society for Industrial and Applied Mathematics
• American Crystallographic Association
• British Crystallographic Association
• Mathematical Association (UK) (Life Member)
• London Mathematical Society

Publications

• L. C. Andrews, H. J. Bernstein, "The Geometry of Niggli Reduction II: BGAOL Embedding Niggli Reduction Arxiv" preprint arXiv: 1305.6561, 2013, http://arXiv.org/pdf/1305.6561.
• K. J. McGill, M. Asadi, M. T. Karakasheva, L. C. Andrews, H. J. Bernstein, "The Geometry of Niggli Reduction III: SAUC Search of Alternate Unit Cells" Arxiv preprint arXiv: 1307.1811, 2013, http://arXiv.org/pdf/1307.1811.
• P. A. Craig, B. Hanson, C. Westin, M. Rosa, H. J. Bernstein, A. Grier, M. Osipovitch, M. MacDonald, G. Dodge, P. Boli, C. Corwin, "Estimation of Protein Function Using Template-Based Alignment of Enzyme Active Sites", BMC Bioinformatics, 2013, submitted.
• L. C. Andrews, H. J. Bernstein, "The Geometry of Niggli Reduction Arxiv" preprint arXiv:1203.5146, 2012. http://arXiv.org/pdf/1203.5146.
• S. E. Mottarella, M. Rosa, A. Bangura, H. J. Bernstein, P. A. Craig, "ConSCRIPT: A RasMol to PyMOL Script Converter," Biochemistry and Molecular Biology Education, submitted August 2010.
• H. J. Bernstein, P. A. Craig, "Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee-Richards surfaces (PGALRS)," J. Appl. Crystallography, 43;2, 2010, pp. 356 -- 361.
• M. T. Dougherty, M. J. Folk, E. Zadok, H. J Bernstein, F. C. Bernstein, K. W. Eliceiri, W. Benger, C. Best, "Unifying biological image formats with HDF5," Comm. ACM 52:10, 2009, pp. 42 -- 47.
• H. J. Bernstein, "Review: important to prevent a return to abuses of the past," Nature, 458:7237, 2009, 404 [doi:10.1038/458404b]
• G. Todorov, H. J. Bernstein, "VCIF2: extended CIF validation software", J. Appl. Cryst. 41, 2008, 808 -- 810 [doi:10.1107/S002188980801385X].
• A. M. Lesk, H. J. Bernstein, F. C. Bernstein, "Molecular Graphics in Structural Biology," book chapter in "Computational Structural Biology " T. Schwede and M. Peitsch, eds., World Scientific Publishing Company, 2008, pp. 729 -- 770.
• H. J. Bernstein, F. C. Bernstein, "Databanks of Macromolecular Structure", chapter 4 in "Database Annotation in Molecular Biology," A. M. Lesk, ed., Wiley, Chichester, UK 2005, pp. 63 -- 79.
• H. J. Bernstein, A. P. Hammersley " Specification of the Crystallographic Binary File (CBF/imgCIF)", chapter 2.3 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 37 -- 43.
• H. J. Bernstein, "The Classification of Image Data", chapter 3.7 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 199 -- 205.
• A. P. Hammersley, H. J. Bernstein, J. D. Westbrook, "Image Dictionary (imgCIF)", chapter 4.6 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 444 -- 458.
• H. J. Bernstein, "General Considerations in Programming CIF Applications", chapter 5.1 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 481 -- 487.
• H. J. Bernstein, S. R. Hall, "CIFtbx: Fortran Tools For Manipulating CIFS", chapter 5.4 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 526 -- 538.
• H. J. Bernstein, P. J. Ellis, "CBFlib: An ANSI C Library for Manipulating Image Data", chapter 5.6 in "International Tables For Crystallography, Volume G: Definition and Exchange of Crystallographic Data," Vol. G, S. R. Hall and B. McMahon, eds., International Union of Crystallography, Springer, Dordrecht, NL, 2005, pp. 544 -- 556.
• P. S. Ivanov, P. Jain, D. Osei-Kuffuor, V. S. Stanev, R.Tripathi, P. N. Zhivkov, H. J. Bernstein, "Comparison of Recent Algorithms for Computing Molecular Surfaces", Proceedings, NCUR 2003, to appear.
• H. J. Bernstein, "Recent changes to RasMol, recombining the variants", Trends in Biological Sciences, September 2000, Vol. 25, No. 9, pp. 453 -- 455.
• H. J. Bernstein, Supplement to "Computer Programming Languages", Encyclopedia of Applied Physics, Update I, VCH Publishers, Inc. , 1999, pp 355 -- 359.
• C. Fockenberg, H. J. Bernstein, G. E. Hall, J. T. Muckerman, J. M. Preses, T. J. Sears, R. E. Weston, Jr., "Repetitively sampled time-of-flight mass spectrometry for gas-phase kinetics studies", Review of Scientific Instruments, Vol. 70, 1999, pp 3259 -- 3264.
• H. J. Bernstein, F. C. Bernstein and P. E. Bourne, "CIF Applications. VIII. pdb2cif: Translating PDB Entries into mmCIF Format," J. Appl. Crystallography, Vol. 31, 1998, pp. 282 -- 295.
• H. J. Bernstein and S. R. Hall, "CIF Applications. VII. CYCLOPS2: Extending the Validation of CIF Data Names," J. Appl. Crystallography, Vol. 31, 1998, 278 -- 281.
• H. J. Bernstein, "Software Engineering", Encyclopedia of Applied Physics , Vol. 18, VCH Publishers, Inc., 1997, pp 305 -- 340.
• S. R. Hall and H. J. Bernstein, "CIF Applications. V. CIFtbx2: Extended Tool Box for Manipulating CIFs", J. Appl. Crystallography, Vol. 29, 1996, pp 598 -- 603.
• J. M. Preses, G. E. Hall, J. T. Muckerman, T. J. Sears, R. E. Weston, C. Guyot, J. C. Hanson, G. W. Flynn and H. J. Bernstein, "A Fourier-Transform Spectrophotometer for Time-Resolved Emission Measurements using a 100-Point Transient Digitizer", Review of Scientific Instruments, 64(1), January 1993, pp 95 -- 102.
• H. J. Bernstein, "Computer Languages", Encyclopedia of Applied Physics , Vol. 4, VCH Publishers, Inc., 1992, pp 163 -- 188.
• H. J. Bernstein, J. Tichler, R. M. Brown, "How to Tell Which Way the Wind is Blowing", BNL Informal Report, BNL-41548, Department of Applied Science, Brookhaven National Laboratory, Upton, New York, July 1988.
• H. J. Bernstein, "Some Comments on Highly Dynamic Network Routing", Technical Report No. 371, Computer Science Department, New York University, May 1988, 11 pp.
• L. C. Andrews and H. J. Bernstein, "Lattices and Reduced Cells as Points in 6-Space and Selection of Bravais Lattice Type by Projections", Acta Cryst., Vol. A44, 1988, pp. 1009 -- 1018.
• H. J. Bernstein, M. Goldstein, "Optimizing Givens' Algorithm for Multiprocessors", SIAM Journal on Scientific and Statistical Computing, Vol. 9, No. 3, May 1988, pp. 601 -- 602.
• H. J. Bernstein, "An Inequality for Self-Adjoint Operators on a Hilbert Space", Proceedings of the AMS, Vol. 100, 1987, pp. 319-321. (Corrigenda in proceedings of the AMS, Vol. 101, 1987, p. 394.)
• H. J. Bernstein, guest editor, "Special Section on Factory Automation and Robotics", Communications of the ACM, Vol. 29 (6) June 1986, pp. 484 -- 522.
• H. J. Bernstein & M. Goldstein, "Parallel Implementation of Bisection for the Calculation of Eigenvalues of Tridiagonal Symmetric Matrices", Computing, Vol. 37, 1986, pp. 85 -- 91.
• H. J. Bernstein, "Constraints in Real Time Data Acquisition and Control," presented at the Symposium on Factory Automation and Robotics, 9-11 September 1985, CIMS/NYU, and as a keynote address at Automation-86, 10-12 March 1986, Houston Texas. Technical Report No. 195, Robotics Research Report No. 59, New York University Dept. of Computer Science, December 1985.
• H. J. Bernstein, "Determining the Shape of a Convex n-sided Polygon by using 2n+k Tactile Probes", New York University, Courant Institute of Mathematical Sciences, Technical Report No. 120, Robotics Report No. 29, June 1984, 13 pp., Information Processing Letters, Vol. 22, April 1986, pp. 255 -- 260.
• H. J. Bernstein, P. G. Lowney & J. T. Schwartz, "SERVOL - Preliminary Proposal for a Programming Language for Real-Time Servo Control", New York University, Courant Institute of Mathematical Sciences, Technical Report No. 120, Robotics Report No. 26, May 1984, 17 pp.
• H. J. Bernstein, "An Accelerated Bisection Method for the Determination of the Eigenvalues of a Symmetric Tridiagonal Matrix," Numer. Math. 43, 153 -- 160, 1984.
• H. J. Bernstein & M. Goldstein, "G22.3023 - Special Topics of Industrial Interest - Network Design and Implementation", Lecture Notes, Spring Semester 1984, 160 pp.
• H. J. Bernstein & M. Goldstein, "G22.2262 - Data Communications", Lecture Notes, Fall Semester 1983, Computer Science Department, Courant Institute of Mathematical Sciences, 160 pp.
• H. J. Bernstein, "Enabling CTS Handshaking on the Intel 8251A USART in Asynchronous Polled Mode", Brookhaven National Laboratory Informal Report, BNL 33617, September 1983, 18 pp.
• H. J. Bernstein, T. S. Clifford, H. R. Connell, W. A. Love, M. H. McKeown, T. C. Nepsee, J. A. Niederer, C. Rebbi, D. R. Stampf, J. L. Tichler, "Interactive Computing Facilities for BNL, Report of a CPC Subcommittee", Brookhaven National Laboratory Informal Report, BNL 33342, March 1983, 14 pp.
• J. Logan, H. J. Bernstein, "A Monte Carlo Simulation of Compton Scattering in Positron Emission Tomography," J. Comput. Assist. Tomography, 7(2), 316-320, April 1983.
• H. J. Bernstein, M. Goldstein, "RINSE - What follows WASHCLOTH", Ultracomputer Note #47, Computer Science Department, New York University, 1982.
• H. J. Bernstein, J. J. Gould, R. Imossi, J. K. Kopp, W. A. Love, S. Ozaki, E. D. Platner, M. A. Kramer, "A Microprocessor-Based Single Board Computer for High Energy Physics Event Pattern Recognition", Topical Conference on the Application of Microprocessors to High Energy Physics Experiments, CERN, Geneva, Switzerland, 4 -- 6 May 1981, poster, BNL #29509.
• L. C. Andrews, H. J. Bernstein, G. A. Pelletier, "A Perturbation Stable Cell Comparison Technique", Acta Cryst., Vol. A36, 1980, pp. 248 -- 252.
• L. C. Andrews, H. J. Bernstein, "The NIH-EPA Chemical Information System", ONLINE, March 1979, pp. 35 -- 49.
• L. C. Andrews, H. J. Bernstein, "The Squared Power Method to Fit a Plane to a Set of Points", Acta Cryst., Vol. A32, 1976, pp. 504 -- 506.
• H. J. Bernstein, "What to do with that Obsolete Computer Center You're Running", Datamation, Vol. 22, No. 11, November 1976, pp. 197 -- 198.
• T. F. Koetzle, L. C. Andrews, F. C. Bernstein, H. J. Bernstein, "CRYSNET: A Network for Crystallographic Computing", ACS Symposium Series, Vol. 19, 1975, pp. 1 -- 8.
• H. J. Bernstein, L. C. Andrews, H. M. Berman, F. C. Bernstein, G. H. Campbell, H. L. Carrell, H. B. Chiang, W. C. Hamilton, D. D. Jones, D. Klunk, T. F. Koetzle, E. F. Meyer Jr., C. N. Morimoto, S. Sevian, R. K. Stodola, M. M. Strongson, T. V. Willoughby, "CRYSNET A Network of Intelligent Remote Graphics Terminals", Second Annual AEC Scientific Computer Information Exchange Meeting, Proceedings of the Technical Program, 1974, pp. 149 -- 161. Brookhaven National Laboratory Report #18803.
• H. J. Bernstein, "Report on Magnetic Tapes and Tape Drives", Applied Mathematics Department, Brookhaven National Laboratory, Document 11.4.1, AMD 657, 1973, 31 pages.
• H. J. Bernstein (as Anon.), "Management Tips from a Programmer", Datamation, Vol. 19, No. 6, June 1973, pp. 204 -- 206.
• H. J. Bernstein, "Compiling Fixed-Point Multiplications", Comm. ACM, Vol. 15, 1972, p 772.
• N. V. Findler, J. L. Pfaltz, H. J. Bernstein, "Four High Level Extensions of FORTRAN IV", Spartan Books, New York, 1972, 391 pages.
• H. J. Bernstein, "317000 Prime Numbers", New York University, March 1970, single copy publication for Courant Institute Library, NYU.
• H. J. Bernstein, "Ludeman's PL/I FORMAC Problem as Handled by SYMBOLANG", SIGSAM Bulletin, #14, January 1970, pp. 19 -- 35.
• H. J. Bernstein, "Stimulus-Response", Analog Science Fiction/Science Fact, September 1969, pp. 92 -- 111.
• H. J. Bernstein, "CCN-Groups of Order Divisible by Three Primes", Proc. AMS, Vol. 22, July 1969, pp. 202 -- 205.
• H. J. Bernstein, "Extension of Hajòs' Factorization Theorem to some Non-Abelian Groups", (doctoral thesis), Comm. Pure and Applied Math., Vol. 21, 1968, pp. 289 -- 311.
• H. J. Bernstein, "Phantasmaplasmagoria," Analog Science Fiction/Science Fact, April 1968, pp. 57 -- 66.
• H. J. Bernstein, O. Moller, E. S. Rapaport, "Machine Factorization of Groups", Mathematical Algorithms, Vol. I, No. 3, 1966, pp. 39 -- 51
• D. Bernstein, H. J. Bernstein, "The Twisted Nose and the Submental Film", Eye, Ear, Nose and Throat Monthly, Vol. 45, 1966, pp. 92 -- 100.
• D. Bernstein, H. J. Bernstein, "Axial Submental Nasal Film", Archives of Otolaryngology, Vol. 82, 1965, pp. 430 -- 432.

Meeting Presentations

• H. J. Bernstein, Managing crystallographic data in facilities using integrated CIF, HDF5 and NeXus talk at Crystallographic Information and Data Management A Satellite Symposium to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 25 August 2013.
• H. J. Bernstein, Software licensing issues and documentation talk at Crystallographic Information and Data Management A Satellite Workshop to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 23 24 August 2013.
• H. J. Bernstein, Report on the CIF/NeXus/HDF5 meeting preceding this Workshop talk at Crystallographic Information and Data Management talk at Crystallographic Information and Data Management A Satellite Workshop to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 23 24 August 2013.
• H. J. Bernstein, Successes and lessons from raw data management talk at Crystallographic Information and Data Management A Satellite Workshop to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 23 24 August 2013.
• H. J. Bernstein, Overlapping Dictionaries: mmCIF and imgCIF talk at NIAC-COMCIFS pre-meeting to Crystallographic Information and Data Management A Satellite Workshop to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 22 August 2013.
• H. J. Bernstein, Specifics of CBF/imgCIF talk at NIAC-COMCIFS pre-meeting to Crystallographic Information and Data Management A Satellite Workshop to the 28th European Crystallographic Meeting, U. of Warwick, Coventry, UK, 22 August 2013.
• G. Dodge, E. N. Arroyo, H. Bernstein, P. Craig, Development and Testing of a Systematic Approach for Com- putational Enzyme Function Determination American Society for Biochemistry and Molecular Biology, 2013 Annual Meeting, Boston, MA, April 20-24, 2013.
• M. T. Karakasheva, M. MacDonald, M. Osipovitch, C. W. Corwin, P. A. Craig, H. J. Bernstein, ProMOL 5 talk, American Crystallographic Association, 2013 Annual Meeting, Honolulu, HI, July 19-24, 2013.
• K. J. McGill, M. Asadi, M. T. Karakasheva, L. C. Andrews, H. J. Bernstein, Unit Cell Search Alternatives (2013), talk, American Crystallographic Association, 2013 Annual Meeting, Honolulu, HI, July 19-24, 2013.
• H. J. Bernstein, J. M. Sloan, G. Winter, T. S. Richter, NeXus International Advisory Committee, Committee on the Maintenance of the CIF Standard, Coping with BIG DATA Image Formats: Integration of CBF, NeXus and HDF5 (2013), poster, American Crystallographic Association, 2013 Annual Meeting, Honolulu, HI, July 19-24, 2013.
• V. A. Kovuri, P. A. Craig, H. J. Bernstein, Recognition of Metal Ions Using ProMOL to Improve Protein Function Assignation, RIT Graduate Student Symposium, July 23, 2013.
• K. Hart, A. Horn, W. Tedla-Boyd, G. Dodge, H. Bernstein, P. Craig, The Biochemical Characterization of the Protein Data Bank Structures 4EZI and 2HRZ by In Silico and In Vitro Quantitative Methods, RIT Undergrad- uate Research Symposium, August 2, 2013.
• H. J. Bernstein, CBF/HDF5/NeXus Integration, talk at DECTRIS Eiger Workshop, Baden, Switzerland, 24-25 January 2013.
• H. J. Bernstein, NSLS-II Data Management Plan,talk at Partnering Data Collection and Reduction in the Beamline Environment workshop, July 27, 2012, Harvard Medical School, Boston, MA.
• A. Bangura, P. A. Craig, H. J. Bernstein, Proposed Protein Function Based on NMR Active Site Templates, poster, American Crystallographic Association, 2012 Annual Meeting, Boston, MA, July 28 August 1, 2012.
• A. Grier, P. A. Craig, H. J. Bernstein, A Database of Predicted Structural Motifs, poster, American Crystallo- graphic Association, 2012 Annual Meeting, Boston, MA, July 28 August 1, 2012.
• M. MacDonald, P. A. Craig, H. J. Bernstein, Using RMSD to Compare the 3D Structures of Active Sites for Protein Function Prediction, poster, American Crystallographic Association, 2012 Annual Meeting, Boston, MA, July 28 August 1, 2012.
• H. J. Bernstein, L. C. Andrews, Bravais General Analysis of Lattices (BGAOL), poster, American Crystallo- graphic Association, 2012 Annual Meeting, Boston, MA, July 28 August 1, 2012.
• G. J. Dodge, C. Corwin, H. J. Bernstein, P. A. Craig, Improving a software system for protein active site determination, poster, American Society for Biochemistry and Molecular Biology, 2012 Annual Meeting, San Diego, CA, April 21 25, 2012.
• H. J. Bernstein, L. C. Andrews, Using Lee-Richards Surfaces to Calculate Close Contacts and Complex Inter- faces, poster MS09.P03, XXII Congress of the International Union of Crystallography, 22 -- 30 August 2011, Madrid, Spain, (see abstract in Acta Cryst. (2011) A67 (on-line supplement), p C269)
• H. J. Bernstein, L. C. Andrews, Lee-Richards Surfaces, Gaussians and Nearest Neighbors, talk session 02.01.05, abstract 02 01 165, ACA 2011, American Crystallographic Association meeting, 28 May 2 June 2011, New Orleans, LA.
• E. Zlateva, H. J. Bernstein, "Local caching to improve effficiency of CIF DDLm function import references in SBEVSL," poster S-179, ACA 2010, American Crystallographic Association meeting, 24 -- 29 July 2010, Chicago, IL.
• P. Craig, M. Rosa, S. Mottarella, G. Dodge, S. Bourne, L. Doucette, H. J. Bernstein, "Function Assignment by Catalytic Site Alignment with ProMOL," poster M-045, ACA 2010, American Crystallographic Association meeting, 24 -- 29 July 2010, Chicago, IL.
• M. Rosa, H. Bernstein, P. Craig, "Enhancements in Motif Preparation and Identiffication in ProMOL," poster M-099, ACA 2010, American Crystallographic Association meeting, 24 -- 29 July 2010, Chicago, IL.
• L. C. Andrews, H. J. Bernstein, "A Pair-Based Approach to Structural Homology Using Quaternion SLERP Averaging and Local Rotations," poster T-100, ACA 2010, American Crystallographic Association meeting, 24 -- 29 July 2010, Chicago, IL.
• H. J. Bernstein, "imgCIF, HDF5, NeXus: Issues in Integration of Images from Multiple Sources "HDF5 as hyperspectral data analysis format" at "HDF5 as hyperspectral data analysis format" Workshop,11 -- 13 January 2010, ESRF, Grenoble, FR.
• L. Doucette, D. Matthews, D., P. A. Craig, H. J. Bernstein, "Optimizing Speed and Accuracy in Visualization of Proteins,", poster (abstract 17), Rochester Institute of Technology 18^th Annual Undergraduate Research Symposium, 7 August 2009, RIT, Rochester, NY.
• M. Rosa, P. A. Craig, H. J. Bernstein, "Lee-Richards Approximation by Intra-Residue Reentrant Surface Exclu- sion," talk (abstract 118), Rochester Institute of Technology 18^th Annual Undergraduate Research Symposium, 7 August 2009, RIT, Rochester, NY.
• S. Mottarella, B. Hanson, C. Westin, P. Craig, H. Bernstein, "RasMol to PyMOL Scripting Language Conversions," poster P-M054 (abstract W0085), ACA 2009, American Crystallographic Association meeting, 25 -- 30 July 2009, Toronto, Canada.
• E. Zlateva, H. Bernstein, N. Darakev, G. McQuillan, J. Ihm, "Use of the Next Generation Dictionary Deffinition Language, DDLm, in CIF validation with CBFlib," poster P-M056 (abstract W0122), ACA 2009, American Crystallographic Association meeting, 25 -- 30 July 2009, Toronto, Canada.
• N. Darakev, H. Bernstein, J. Ihm, G. McQuillan, E. Zlateva, P. Craig, L. Grell, "New Molecular Graphics Movie Scripting Features under SBEVSL," poster P-M057 (abstract W0124), ACA 2009, American Crystallographic Association meeting, 25 -- 30 July 2009, Toronto, Canada.
• H. J. Bernstein, P. Craig, "A New Approach to Identiffication of Surface Residues," poster P-T006 (abstract W0121), ACA 2009, American Crystallographic Association meeting, 25 -- 30 July 2009, Toronto, Canada.
• P. Craig, B. Hanson, C. Westin, C. Wischmeyer, H. Bernstein, "Local Area Structural Alignment with ProMOL," talk (abstract W0084), ACA 2009, American Crystallographic Association meeting, 25 -- 30 July 2009, Toronto, Canada.
• H. J. Bernstein, "Transition to object-oriented data representations: Interconversion between CIF and other formats," invited talk MS.96.3, XXI Congress of the International Union for Crystallography, 23 -- 31 August 2008, Osaka, Japan, (see abstract in Acta Cryst. (2008) A64 (on-line supplement), p C160)
• H. J. Bernstein, G. Darakev, N. Darakev, J. Jemilawon, G. McQuillan, G. Todorov, P. A. Craig, S. E. Mottarella, C. Wischmeyer, "A simpliffied uniffied approach for animations and movies using SBEVSL," poster P01.02.81, XXI Congress of the International Union for Crystallography, 23 -- 31 August 2008, Osaka, Japan, (see abstract in Acta Cryst. (2008) A64 (on-line supplement), p C195)
• H. J. Bernstein, I. Awuah Asiamah, G. Darakev, N. Darakev, J. Jemilawon, N. Jia, P. Kamburov, G. McQuillan, G. Todorov, "SAXS, Lee-Richards surfaces and a simpliffied command set for maps," poster MP039 (abstract W0070), ACA 2008, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN.
• P. A. Craig, S. E. Mottarella, C. Wischmeyer, H. J. Bernstein, I. Awuah Asiamah, D. Boycheva, G. Darakev, N. Darakev, P. Gozo, J. Jemilawon, "Using RasMol, PyMol and Jmol with the Structural Biology Extensible Visualization Scripting Langauge (SBEVSL)," poster MP054 (abstract W0073), ACA 2008, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN.
• S. Mottarella, B. Hanson, C. Westin, P. Craig, H. Bernstein, "A Rasmol to PyMOL Translator," poster TP161 (abstract W0049), ACA 2008, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN.
• C. Wischmeyer, P. Craig, H. Bernstein, "Homology Exploration with ProMOL," poster SP169 (abstract W0050), ACA 2008, American Crystallographic Association Meeting, 31 May -- 5 June 2008, Knoxville, TN.
• H. J. Bernstein, "Progress in adoption of imgCIF and integration with NeXus, "presentation at imgCIF workshop, Brookhaven National Laboratory, 22 May 2008
• H. J. Bernstein, "Routing Students in Computer Science", presentation for "Preparing the Computing Workforce; the Interface Between K-12 and College" panel at CCSCE 2007 meeting of the Consortium for Computing Sciences in Colleges -- Eastern Region, 12 -- 13 October 2007, St. Joseph's College, Patchogue, NY, with panel abstract in H. J. Bernstein, J. S. Kay, W. McAllister, R. K. Raj, "Preparing the computing workforce: the interface between K-12 and college," Journal of Computing Sciences in Colleges, 23, 2008, pp. 175 -- 178
• H. J. Bernstein, "ImgCIF and the Interaction with NeXus", workshop presentation at imgCIF Workshop, 17 August 2007, Diamond Light Source, Chilton, UK, organized in conjunction with BSR 2007
• H. J. Bernstein, "imgCIF Progress, A Report to the Community", poster at poster session B, 9th International Conference on Biology and Synchrotron Radiation (BSR 2007), 13-17 August 2007, Manchester, UK. Supplemented by oral presentation in imgCIF workshop, 14 August 2007 at BSR 2007, Manchester, UK
• J. Jemilawon, I. Awuah Asiamah, H. J. Bernstein, G. Darakev, N. Darakev, P. Kamburov, "Use of CBFlib for Map Support", poster, poster session B, 9th International Conference on Biology and Synchrotron Radiation (BSR 2007), 13-17 August 2007, Manchester, UK
• G. Darakev, H. J. Bernstein, "Achieving portability for synchrotron images using NeXus and XML", poster, poster session B, 9th International Conference on Biology and Synchrotron Radiation (BSR 2007), 13-17 August 2007, Manchester, UK
• H. J. Bernstein, I. Awuah Asiamah, G.Darakev, J. Jemilawon, P. Kamburov, "Suppor t for Maps in RasMol", poster TP174 (abstract W0059), ACA 2007, American Crystallographic Association Meeting 2007 Meeting, 21-26 July 2007, Salt Lake City, UT.
• C. Westin, B. Hanson, H.J. Bernstein, I. Awuah Asiamah, D. Boycheva, G. Darakev, J. Jemilawon, N. Jia, P. Kamburov, G. Todorov, P.A. Craig, S. Mottarella, "SBEVSL: Communicating Scripts Between Molecular Visualization Programs", poster TP172 (abstract E0003), ACA 2007, American Crystallographic Association Meeting 2007 Meeting, 21-26 July 2007, Salt Lake City, UT.
• H. J. Bernstein, "CIF, mmCIF, imgCIF and more: Reducing Friction in PX Sychrotron Image Data Acquisition", workshop presentation, session 2A, "Standards for data format and management," CGW 2007, at Second International CrystalGrid Workshop on Crystallographic Data Management, 26-28 April 2007, Bloomington, IN
• H. J. Bernstein, "CIF, mmCIF, imgCIF and more: Reducing Friction in Managing Data in Structural Biology" given on 12 January 2007, Paul Scherrer Institut, Villigen CH and 17 January 2007, European Synchrotron Radiation Facility, Genoble, FR
• H. J. Bernstein, "Notes on Computer Science Education -- Is it Broken?", panel presentation, session 2A. "Panel: Broken or Not? Fixing Undergraduate Computing Education in a Multi-Disciplinary World," CCSCNE 2007 meeting of the Consortium for Computing Sciences in Colleges -- Northeastern Region, 20-21 April 2007, Rochester Institute of Technology, Rochester, NY with abstract in R. K. Raj, J.S. Kay, H. J. Bernstein, C. Okasaki, J. Forbes, V. Teller, "Broken or not?: fixing undergraduate computing education in a multi-disciplinary world", Journal of Computing Sciences in Colleges 22, 2007 pp. 53 -- 55.
• R. M. Sweet, H. J. Bernstein, "imgCIF: The Management of Synchrotron Image Data", workshop WK.02 (abstract E0025), ACA 2006, American Crystallographic Association Meeting, 22-27 July 2006, Honolulu, HI.
• G. Todorov, K. Z. Mitev, H. J. Bernstein, "Extended CIF Validation Software", poster S-P083 (abstract W0169), ACA 2006, American Crystallographic Association Meeting, 22 -- 27 July 2006, Honolulu, HI.
• G. Darakev, G. Todorov, V. Litchev, K. Z. Mitev, H. J. Bernstein, "NeXus with Binary XML - Effficient Support of Binary Data in the XML Implementation of the NeXus File Format", poster M-P156 (abstract W0165), ACA 2006, American Crystallographic Association Meeting, 22 -- 27 July 2006, Honolulu, HI.
• K. Mitev, H. Todorov, H. J. Bernstein, "CIFFOLD: Managing Long Lines in CIF", presentation MS86.30.3 at XX Congress of the International Union of Crystallography, 23-31 August 2005, Florence, IT, (see abstract in Acta Cryst. (2005) A61 (on-line supplement), p C109)
• H. J. Bernstein, F. C. Bernstein, "The PDB Format in the 21st Century, a Modest Proposal", poster P.24.08.2 at XX Congress of the International Union of Crystallography, 23 -- 31 August 2005, Florence, IT, (see abstract in Acta Cryst. (2005) A61 (on-line supplement), p C484)
• P. N. Zhivkov, H. J. Bernstein, "Approximating Short-Range Lee-Richards Molecular Surfaces by Blurring" poster abstract W0037, ACA 2004, American Crystallographic Association Meeting, 17 -- 22 July 2004, Chicago, IL.
• H. J. Bernstein and F. C. Bernstein, "Molecular Graphics Color Management for the Colorblind", presentation and poster abstract P131, ACA 2003, American Crystallographic Association Meeting, 26 -- 31 July 2003, Covington, KY.
• H. J. Bernstein and F. C. Bernstein, "Extension of RasMol to Display Surfaces, to Handle CML/XML and other new Features" presentation, XIX Congress and General Assembly of the International Union of Crystallography, Geneva, Switzerland, August 6 -- 15, 2002 (see abstract in Acta Cryst. (2002) A58 (Supplement), C217)
• H. J. Bernstein and F. C. Bernstein, "Yaxdf and the Interaction between CIF and XML" presentation at XIX Congress and General Assembly of the International Union of Crystallography, Geneva, Switzerland, August 6 -- 15, 2002 (see abstract in Acta Cryst. (2002) A58 (Supplement), C217)
• H.J. Bernstein and F.C. Bernstein, "xmlCIF: A Proposal for Faithful Translation Between XML and Extended CIF", poster (abstract E0009), ACA 2000, American Crystallographic Association Meeting, St. Paul, MN, 22 -- 27 July 2000.
• F. C. Bernstein and H. J. Bernstein, "Graphical Representation of Alternate Conformers", poster session, XVIII IUCr Congress & General Assembly, Glasgow, Scotland, 4 -- 13 August 1999, and Acta Cryst, A55 (Supplement) 264.
• H. J. Bernstein, P. J. Ellis, A. P. Hammersley, A. J. Howard, J. W. Pflugrath, R. M. Sweet, "Proposed Crystallographic Binary File and Image-suppor ting CIF with API and Dictionary", poster session, XVIII IUCr Congress & General Assembly, Glasgow, Scotland, 4 -- 13 August 1999, and Acta Cryst, A55 (Supplement) 235.
• H. J. Bernstein and F. C. Bernstein, "Recent Developments in Software Tools for CIF and mmCIF", presentation, ACA 2008, American Crystallographic Association Meeting, Arlington, VA, 18 -- 23 July 1998.
• H. J. Bernstein, F. C. Bernstein, "Converting Fortran Applications for use with CIF", invited presentation at mmCIF Software Developers' Workshop, Rutgers, 17 -- 19 October 1997.
• J. Westbrook, D. Argentar, H. M. Berman, H. Bernstein, F. Bernstein, J. Biggs, P. Bourne, I. D. Brown, S. Bryant, J. Fait, P. Edgington, P. Fitzgerald, A. Hammersley, P. Keller, B. McMahon, P. Murray-Rust, O. Ritter, R. Sayle, J. Thornton, B. Toby, E. Ulrich, K. Watenpaugh, S. Wodak, "CIF Application Developers' Workshop", (Abstract E253), ACA 1997, American Crystallographic Association Meeting, St. Louis, MO, 19 -- 25 July 1997. Served with J. Westbrook as co-chair of the session.
• F. C. Bernstein and H. J. Bernstein, "Data Representation of Disorder and Alternate Conformations in Macromolecular Structures", poster (abstract E116), ACA 1997, American Crystallographic Association Meeting, St. Louis, MO, 19 -- 25 July 1997.
• F. C. Bernstein, H. J. Bernstein and P. E. Bourne, "An Introduction to mmCIF: Conversion between PDB Format and mmCIF", poster, 24th Aharon Katzir-Katchalsky Conference on Bioinformatics -- Structure, 17 -- 21 November 1996.
• H. J. Bernstein and L. C. Andrews, "Software for Lattice Identiffication in G-6", invited presentation for Seattle IUCr meeting, 7 -- 17 August 1996.
• H. J. Bernstein, F. C. Bernstein and P. E. Bourne, "Moving Between mmCIF and PDB Format", poster at BCA Meeting, Cambridge England, 1 -- 4 April 1996.
• F. C. Bernstein and H. J. Bernstein, "Translating mmCIF Data into PDB Entries", invited presentation for CIF workshop at Seattle IUCr meeting, 7 -- 17 August 1996.
• P. E. Bourne, H. J. Bernstein and F. C. Bernstein, "Translating PDB Entries into mmCIF", invited presentation for CIF workshop at Seattle IUCr meeting, 7 -- 17 August 1996.
• H. J. Bernstein and S. R. Hall, "Reading, Writing and Validating CIFs using CIFtbx2 AND CYCLOPS", invited presentation for CIF workshop at Seattle IUCr meeting, 7 -- 17 August 1996.
• L. C. Andrews and H. J. Bernstein, "Bravais Lattice Invariants", poster session, ACA 1993, American Crystallographic Association Meeting, Albuquerque, New Mexico, May 1993, and Acta Cryst., A51, 1995, pp. 413 -- 416.
• A. P. Hull, P. A. Michael, H. J. Bernstein, "A Real-Time Stack Radioactivity Monitoring System and Dose Projection Program", a presentation by A. Hull to the 23rd DOE/NRC Nuclear Air Cleaning and Treatment Conference, Buffalo, New York July 25-28, 1994, proceedings available at http://www.eh.doe.gov/hepa/Nureg 23rd/nureg.html, session 7, pp. 259 -- 268.
• H. J. Bernstein, "Brookhaven National Laboratory's Technical Assistance to the NRC for ???Radioactive Materials Released from Nuclear Power Plants' ", a presentation to the Nuclear Utility Meteorological Data Users Group Meeting (NUMUG), April 28 -- 30, 1993, Boston, MA [note: based on work by J. Tichler, K. Doty, J. Congemi]
• J. L. Tichler, H. J. Bernstein, S. F. Bobrowski, R.B. Melton, A. P. Campbell, D. M. Edwards, P. Kanciruk and P. Singley, "Design and Implementation of a Computer Based Site Operations Log for the ARM Program", presented at SDM 92, A Planning Workshop, Scientiffic Data Management Workshop, 1992, The Role of Metadata in Managing Large Environmental Sciences Data Sets, Salt Lake City, UT, November 3 -- 5, 1992.
• L. C. Andrews and H. J. Bernstein, "The G-6 Method of Bravais Lattice Determination", poster session, ACA 1989, American Crystallographic Association Meeting, Seattle Washington, July 1989.
• H. J. Bernstein, "Where we Stand in Data Communications for Engineering R&D", talk presented at 1987 ASME International Computers in Engineering Conference, August 9 -- 13, 1987, in panel session 41 on "Information and Access Networks for Supercomputing", 12 August 1987.
• H. J. Bernstein, "Digital Communications", presented as an invited talk in the 1986 New Horizons in Physics and Engineering Lecture Series on TelecommunicationsAmerican Crystallographic Association Meeting College at New Paltz, State University of New York, 9 October 1986. H. J. Bernstein, "A Tutorial on Maximum Entropy", presented as an invited talk, ACA 1986, American Crystallographic Association Meeting, 6 February 1986, Institute for Cancer Research, Fox Chase Center, Philadelphia, Pennsylvania.
• D. R. Christman, H. L. Atkins, H. J. Bernstein, J. S. Fowler, B. M. Gallagher, T. Ido, R. M. Lambrecht, R. R. MacGregor, M. Reivich, T. Ruth, P. Som & A. P. Wolf, "The Use of PETT III at Brookhaven", First International Symposium on Positron Emission Tomography, 1 -- 3 June 1978, Montreal, Canada.
• J. Tichler, H. Bernstein, R. M. Brown, P. Daum, "A Data Acquisition System for Environmental Monitoring Aboard a Twin-Engined Aircraft", Proceedings of the Fifth Symposium on Meteorological Observations and Instrumentation, April 11 -- 15, 1983, Toronto, Ont., Canada.
• E. F. Meyer Jr., C. N. Morimoto, J. Villarreal, H. M. Berman, H. L. Carrell, R. K. Stodola, T. F. Koetzle, L. C. Andrews, F. C. Bernstein, H. J. Bernstein, "CRYSNET, A Crystallographic Computing Network with Interactive Graphics Display", FASEB Meeting, Aspen Colorado, June 1974.