Herbert J. Bernstein

	Contact Information	Research Professsor Computer Science Department 1438 Computer Science University at Stony Brook Stony Brook, NY 11794-4400 +1-631-632-8959 yaya@cs.sunysb.edu
	Research Interests	bioinformatics, data representation, molecular graphics, laboratory automation, numerical linear algebra, networking and data communications, software engineering
	Teaching	Fall 2001: CSE101, CSE103

Note: I am at SUNY only part time for the Fall 2001 semester (mainly Monday and Friday afternoons and all days Wednesdays), but I can be reached by email (yaya@cs.sunysb.edu or yaya@bernstein-plus-sons.com) at any time and, if calling me at +1-631-632-8959 does not work, try me at home +1-631-286-1339. In a dire emergency, try my cell phone +1-631-428-1397.

Research-Related Web Sites

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

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, "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 Haj˜s' Factorization Theorem to some Non-Abelian Groups", (doctoral thesis), Comm. Pure and Applied Math., Vol. 21, 1968, pp. 289Ñ311.
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 and F.C. Bernstein, "xmlCIF: A Proposal for Faithful Translation Between XML and Extended CIF", poster at St. Paul ACA Meeting, 22-27 July 2000, Abstract E0009.
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, Vol A55 supplement.
H. J. Bernstein, P. J. Ellis, A. P. Hammersley, A. J. Howard, J. W. Pflugrath, R. M. Sweet, "Proposed Crystallographic Binary File and Image-supportin CIF with API and Dictionary", poster session, XVIII IUCr Congress & General Assembly, Glasgow, Scotland, 4-13 August 1999, and Acta Cryst, Vol A55 supplement.
H. J. Bernstein and F. C. Bernstein, "Recent Developments in Software Tools for CIF and mmCIF", presentation at 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," at St. Louis ACA Meeting, 19-25 July 1997, Abstract E253. 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 at St. Louis ACA Meeting, 19-25 July 1997, Abstract E116.
F. C. Bernstein, H. J. Bernstein and P. E., Bourne, "An Introduction to mmCIF: Conversion between PDB Format and mmCIF", poster at the 24th Aharon Katzir-Katchalsky Conference on Bioinformatics - Structure, 17-21 November 1996.
H. J. Bernstein and L. C. Andrews, "Software for Lattice Identification 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 Meeting, Albuquerque, New Mexico, May 1993, and Acta Cryst., Vol. A51, 1995, pp. 413-416.
H. J. Bernstein, "Brookhaven National LaboratoryÕs Technical Assistance to the NRC for ÔRadioactive Materials Released from Nuclear Power PlantsÕ", 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, Scientific 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 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 Telecommunications at the 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 at the Institute for Cancer Research, Fox Chase Center, Philadelphia, Pennsylvania, 6 February 1986.
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, Montreal, Canada, 1-3 June 1978.
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.
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.

Page updated 6 September 2001