6/4/02
DOCUMENT TYPES
1.
published articles and conference papers
a. journal articles:
SCOPE: articles in edited or peer-reviewed journals and magazines. If possible, include
DOI.
b. conference papers:
SCOPE: formal papers, usually peer-reviewed. For presentations based on slides, notes,
or informal text, use type 2.
2.
presentations, talks, and seminars:
SCOPE: used for informal presentations usually without peer-review. May be given to
informal workshops (contrasted with formal courses and tutorials, for which use type 3).
Links may be to slides, notes, webcast, or abstract. No subtypes.
3.
courses, tutorials, and workshops: formal courses, may be for credit, requiring students to enroll or
register.
a. courses:
SCOPE: use where sponsored by an academic or professional organization, where credit
is provided, and/or where instruction takes place over long term.
b. tutorials or workshops:
SCOPE: use for more informal, usually short-term instruction of one or two days, often
given within a formal conference setting.
4.
reports, documents, and preprints
a. reports (include technical reports):
SCOPE: use for annual reports, technical reports with or without numbering, and
planning or progress reports, generally not peer-reviewed.
b. documents (include patents, grant documents):
SCOPE: use for other documents including patents and grant documents such as grant
abstracts.
c. Preprints:
SCOPE: use for preprints such as those deposited in eprint and preprint repositories (e.g.
arXiv), as well as informal preprints issued prior to formal publication.
5.
conferences and conference proceedings
a. conferences
SCOPE: use for web sites for conferences where no proceedings exist.
b. conference proceedings
SCOPE: use for proceedings of conferences whether published digitally or in print.
6.
books and book chapters
a. books
b. book chapters
7.
theses
SCOPE: use for academic theses and dissertations.
RECORD 1:
Type 1: published articles and conference proceedings
Subtype: published article
Author 1: Baldridge, K. K.
Author 1 email: kimb@sdsc.edu
Author 2: Siegel, J. S.
Organization 1: SDSC
Organization 2: UCSD Department of Biochemistry and Chemistry
Title: Quantum mechanical designs toward planar delocalized cyclooctatetraene: A new target for synthesis
Year: 2001
Journal/Conference Name: Journal of the American Chemical Society
Volume: 123
Issue: 8
Pages: 1755-1759
Keywords:
generalized gradient approximation
bond localization
transition-state system
exchange
ring
construction
derivatives
energetics
alternation
Abstract:
Ab initio and hybrid density functional quantum mechanical computation are applied to the structure and
energetics of a series of annelated cyclooctatetraenes. Tetrakis-cyclobuteno, perfluorocyclobuteno or
bicyclo[2.1.1]hexeno annelations result in planar structures with distinct exo and endo valence tautomers of the
double bonded cycle. The contribution of each basic annelation to the exo/endo relative energy is estimated. An
additivity scheme for approximating the energy of a mixed system is developed and compared to the quantum
mechanical prediction. Bis bicyclic annelation to the a and d positions creates "valence tautomeric frustration"
and strongly perturbs the molecular structure. This phenomenon leads to a general design for a planar
cyclooctatetraenes where the "delocalized" diradicaloid state is the minimum energy form. These compounds
are seen as excellent targets for chemical synthesis.
ID numbers: DOI: 10.1021/ja003383+
URL: http://pubs.acs.org/journals/jacsat/article.cgi/jacsat/2001/123/i08/pdf/ja003383+.pdf
END RECORD 1
RECORD 2:
Type 1: published articles and conference papers
Sub-Type: published article
Author 1: Baldridge, Kim K.
Author 1 email: kimb@sdsc.edu
Organization 1: SDSC
Title: Computers expanding impact on chemistry
Year: 2001
Journal/Conference: Chemical & Engineering News
Volume: 79
Issue: 13
Pages: 265
Keywords:
Abstract:
ID numbers:
URL:
END RECORD 2
RECORD 3:
Type 1: published articles and conference proceedings
Sub-Type: published conference paper
Author 1: Smith, C. M.
Author 1 email:
Author 2: Baldridge, K. K.
Author 2 email: kimb@sdsc.edu
Author 3: Arzberger, P.
Author 3 email: parzberg@sdsc.edu
Organization: SDSC
Title: National Biomedical Computation Resource
Journal/Conference: FASEB Journal
Year: 2001
Volume: 15
Issue: 5
Pages: A-880
Keywords:
Abstract:
ID numbers:
URL:
END RECORD 3
RECORD 4:
Type 2: presentations, talks, seminars, and workshops
Author 1: Pezzoli, Keith
Author 1 email:
Organization: SDSC
Title: Information Technology Research at the Frontiers of Regional Ecology
Series: Computational Science Seminar Series
Year: 2002
Month: February
Day: 27
Location: San Diego Supercomputer Center
Keywords:
regional ecology
Abstract:
Regional ecology is a multidisciplinary domain of integrated theory building and practice aimed at
conceptualizing and promoting sustainable development. The frontiers of regional ecology lie at the nexus of
metropolitan (city-region) planning, economic geography, environmental science, and innovative developments
in information and communications technology. This presentation provides an overview of ITR challenges
raised by regional ecology and the quest for sustainable development. Ongoing efforts in the San Diego-Tijuana
border region serve as a point of reference. Topics covered include the role of ITR in: (1) mapping and
integrating the ontological domains of sustainability science, (2) enabling knowledge-based integration and
navigation of distributed regional environmental data, including heterogeneous spatial information and
knowledge across jurisdictional and political boundaries, (3) creating planning and decision-support tools, and
(4) promoting social justice and equity through university-based knowledge-action collaboratives.
ID number:
URL: http://www.sdsc.edu/CSSS/forums/pezzoli2002.html
END RECORD 4
RECORD 5:
TYPE 3: courses and tutorials
Subtype: tutorial
Author 1: Rajasekar, Arcot
Author 1 email: sekar@sdsc.edu
Organization: SDSC
Title: SRB Data Grid and Collection Management
Year: 2002
Month: March
Day: 6
Keywords:
MCAT
SRB
MySRB
Abstract:
The Storage Resource Broker (SRB) developed at the San Diego Supercomputer Center, provides federation
and uniform access to distributed and diverse storage resources in a heterogeneous computing environment.
The Metadata Catalog (MCAT) holds systemic and application- or domain-dependent metadata about systemic
and application- or domain-dependent metadata about the resources and datasets, methods and users that are
being brokered by SRB. Together, the SRB and the MCAT provide a scalable information discovery and access
system for publishing and computing with scientific data and metadata.
ID:
URL: http://www.npaci.edu/ahm2002/schedule.html
END RECORD 5
RECORD 6:
TYPE 3: courses and tutorials
Subtype: course
Author 1: Baldridge, Kim K.
Author 1 email: kimb@sdsc.edu
Organization: SDSC
Title: Chemistry 245, Structure and Properties of Organic Molecules
Year: 2001
Month:
Day:
Keywords:
Abstract:
This course is being offered to undergraduate and graduate students with an interest in detailed analysis of the
structure and property of organic molecules. After a brief introduction and background in computational theory,
several topics will be addressed, including structure/energy relationships and the manifestation in properties of
molecular systems. The class will take place in an actual computer lab to give maximum hands on experience.
ID:
URL:
END RECORD 6
RECORD 7:
TYPE 4: reports, documents, and preprints
SUBTYPE: document
Author 1: Bourne, P. E.
Author 1 email: bourne@sdsc.edu
Author 2: Kim K. Baldridge
Organization 1: SDSC-Integrative Biology
Organization 2: Protein Data Bank
Title: Computational Quantum Mechanical Biological Framework in Conjunction with the Protein Data Bank
Year: 2000
Month: September
Day:
Funding/Sponsoring Agency: NSF
Keywords:
Abstract:
Biological systems are integrated complex assemblies of macromolecules that use chemical energy to sustain
life. As such, their properties area function of their physicochemical parameters such as solubility, lipophilicity,
electronic effects, ionization, and stereochemistry, that have profound influence on the chemistry and
biochemistry of the complex.This project develops a computational platform that integrates 1. physically-based
computational and analytical modeling using QM techniques, 2. experimental databases, 3. computational
analysis tools, and 4. visualization/manipulation interfaces, in order to create a transparent and common
interface for the use of these now relatively disparate set of tools. This infrastructure will provide a database and
integrate associated tools that allows the user to focus on the principles of stereochemistry, chemical synthesis,
computational structure prediction, and physical analysis as applied to molecular recognition, biomolecular
conformational analysis, and supramolecular chemistry. The end result will impact biologists and biochemists
working in areas such as bioorganic chemistry, medicinal chemistry, enzyme structure and function, and nucleic
acid recognition.
ID: NSF 00-78296
URL: https://www.fastlane.nsf.gov/servlet/showaward?award=0078296
END RECORD 7
RECORD 8:
TYPE 4: reports, documents, and preprints
SUBTYPE: report
Author 1: Bourne, P. E.
Author 1 email: bourne@sdsc.edu
Organization 1: Protein Data Bank
Organization 2: Research Collaboratory for Structural Bioinformatics
Organization 3: National Institute for Standards and Technology
Organization 4: San Diego Supercomputer Center
Title: Protein Data Bank Annual Report
Year: 2000
Month:
Day:
Funding/Sponsoring Agency:
Keywords:
Abstract:
ID: SDSC TR-2000-2
URL: http://www.sdsc.edu/TR/Tech_rept_PDB_annual_2_00.pdf
END RECORD 8
RECORD 9:
TYPE 4: reports, documents, and preprints
SUBTYPE: preprints
Author 1: Aspnes, James
Author 1 email:
Author 2: Hartling, Julia
Author 3: Kao, Ming-Yang
Author 3 email: kao@cs.yale.edu
Author 4: Kim, Junhyong
Author 5: Shah, Gauri
Organization: Protein Data Bank
Title: Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model
Year: 2001
Month: January
Day: 17
Keywords:
Abstract:
In modern biology, one of the most important research problems is to understand how protein sequences fold
into their native 3D structures. To investigate this problem at a high level, one wishes to analyze the protein
landscapes, i.e., the structures of the space of all protein sequences and their native 3D structures. Perhaps the
most basic computational problem at this level is to take a target 3D structure as input and design a fittest
protein sequence with respect to one or more fitness functions of the target 3D structure. We develop a toolbox
of combinatorial techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan,
and Dill. The toolbox is based on linear programming, network flow, and a linear-size representation of all
minimum cuts of a network. It not only substantially expands the network flow technique for protein sequence
design in Kleinberg's seminal work but also is applicable to a considerably broader collection of computational
problems than those considered by Kleinberg. We have used this toolbox to obtain a number of efficient
algorithms and hardness results. We have further used the algorithms to analyze 3D structures drawn from the
Protein Data Bank and have discovered some novel relationships between such native 3D structures and the
Grand Canonical model.
ID:
URL: http://arxiv.org/abs/cs.CE/0101015
END RECORD 9
RECORD 10:
TYPE 5: conferences and conference proceedings
SUBTYPE: conference
Title: NPACI All Hands Meeting: AHM2002: Building the TeraGrid: Architecture - Middleware and Applications
Organization: NPACI
Year: 2002
Month: March
Day: 6-9
Keywords:
Abstract:
The mission of the meeting is to share information on the TeraGrid -- its architecture, middleware, and
applications. Anyone is eligible to attend (including NCSA, PSC, and the vendor community).
ID:
URL: http://www.npaci.edu/ahm2002/
END RECORD 10
RECORD 11:
TYPE 5: conferences and conference proceedings
SUBTYPE: conference proceedings
Author/Editor 1: Helly, John
Author/Editor 1 email: helly@sdsc.edu
Author/Editor 2: Case, Ted
Author/Editor 3: Davis, Frank
Author/Editor 4: Levin, Simon
Author/Editor 5: Michener, William
Organization 1: SDSC
Organization 2: National Center for Ecological Analysis
Organization 3: NCSA
Title: The State of Computational Ecology
Year: 1995
Month: September
Day:
Keywords:
Abstract:
Computational ecology is a field devoted to the quantitative description and analysis of ecological systems
using empirical data, mathematical models (including statistical models), and computational technology. While
the components of this field are not new, there is a new emphasis on the integrated treatment of the area. To a
large degree, this emphasis is precipitated by the expansion of our local, national, and international
computational infrastructure, coupled with the heightened social awareness of ecological and environmental
issues and its effects on research funding. In an attempt to consolidate what is known about the state-ofpractice in computational ecology, a workshop was held gathering together ecologists and computer scientists
for the purpose of identifying those technology issues which impede the progress of ecological research. This
workshop was held at the San Diego Supercomputer Center in September 1995. The results of the workshop
are expressed in three areas: data management, visualization, and modeling. Common to these areas is the
need to develop standards to facilitate the sharing of data, the comparison of results, and the integration of
model components. Unique to the problem of data sharing is the issue of the proprietary nature of research data
and the lack of institutional incentives for data sharing along with the usual issues of intellectual property. The
use of visualization continues to be inhibited by the highly specialized knowledge still required to effectively
utilize current visualization packages along with fundamental questions such as how should statistical error be
represented in visual presentations. The modeling community is challenged by questions such as how multiscale, multi-resolution models may be integrated across disciplines, as well as the desire for collections of
standard realizations of model components to minimize redundant software development and facilitate the
comparison of modeling analyses.
ID:
URL: http://www.sdsc.edu/compeco_workshop/report/helly_publication.html
END RECORD 11
RECORD 12:
TYPE 6: books and book chapters
SUBTYPE: book
Author/Editor 1: Bourne, Philip E.
Author/Editor 1 email: bourne@sdsc.edu
Organization: SDSC
Title: A cookbook for serving the Internet : UNIX version
Year: 1997
Publisher: Prentice-Hall
Keywords:
Abstract:
Written especially for UNIX professionals, this is a step-by-step guide to setting up Internet information servers.
Formatted like a cookbook for easy use, this text covers all Internet information services, including the World
Wide Web, WAIS, Gopher, Archie, ftp, listserver and more. readers learn how to get the latest versions of the
software they'll need, while grasping an understanding of all their options for graphics, interactivity and security.
ID Numbers: ISBN 0135199921
URL:
END RECORD 12
RECORD 13:
TYPE 6: books and book chapters
SUBTYPE: book chapter
Author 1: Baldridge, Kim K
Author 1 email: kimb@sdsc.edu
Author 2: Jensen, J.H
Author 3: Matsunaga, N.
Author 4: Schmidt, M.W.
Author 5: Gordon, M.S.
Author 6: Windus, T.L.
Author 7: Boatz, J.A.
Author 8: Cundari, T.
Organization: SDSC
Chapter Title: Applications of Parallel GAMESS
Pages:
Book Title: Parallel Computing in Computational Chemistry
Editor: Mattson, Timothy G.
Year: 1995
Publisher: American Chemical Society
Keywords:
Abstract:
ID Numbers: ISBN: 0841231664
URL:
END RECORD 13
RECORD 14
TYPE 7: theses
Author: Bailey, Timothy L.
Author email: tbailey@sdsc.edu
Organization 1: SDSC
Organization 2: UCSD
Title: Discovering motifs in DNA and protein sequences: The approximate common substring problem
Year: 1995
Department: UCSD Department of Computer Science and Engineering
Keyword:
Abstract:
ID:
URL: http://www.sdsc.edu/~tbailey/papers/thesis.ps
END RECORD 14