ACRL News Issue (B) of College & Research Libraries


112 / C&RL News •  February 2002

I N T E R N E T  R E S O U R C E S

Computational science

An Internet introduction

by Anna Keller Gold

F rom the Web pages o f professional or­ganizations1 to job advertisements in sci­
entific journals2 to the pages of the New York 
Times3 there is evidence that, more and more, 
sciences are becoming computational. Com­
putational science has becom e “an equal and 
indispensable partner, along with theory and 
experiment, in the advance of scientific knowl­
edge and engineering practice.”4

It is an important part of biology and medi­
cine, chemistry, engineering, mathematics, 
physics, astronomy and space science, earth 
and environmental science, linguistics, and 
every other field in which data exist in mas­
sive quantities, and research problems exist that 
are “otherwise too big, too small, too expen­
sive, too scarce, or too inaccessible to study.”5 

The subject of computational science is 
diffuse, and no single portal exists that brings 
together its many facets. Thus the goal of this 
guide is to offer a sampling o f Web sites that 
introduce the subject or relate to the tools 
used in computational science, its diverse 
applications, and the variety o f people and 
organizations involved in computational sci­
ence instruction and research.

C o m pu tatio n al science, inform atics, 
and lib rary p ro fe ssio n als
Librarians in research libraries are continu­
ally faced with new disciplines and research

p ro gram s sty led  as “in fo r m a tic s ”; b io - 
informatics and medical informatics are among 
the most familiar o f these.

Along with “com p u tatio n al s c ie n c e ,” 
“inform atics” is a term used to describe the 
scie n ce  o f com bining the use o f com puta­
tional techniqu es (algorithm s), tools (sp e ­
cialized com puters with various visualiza­
tion systems, including the Web and data­
bases, data w arehousing, and other soft­
w a re), and m ath em atics (m o d els from  
wavelets to partial differential equations to 
quantum lattices and cellular autom ata) in 
the analysis o f scientific data.

Developments in computational science 
will place new demands on the inform a­
tion m anagem ent skills o f researchers and 
librarians alike and will continue to offer 
challenging opportunities for collaborations 
betw een scientists and information profes­
sionals.

Startin g points, tu to rials, and on lin e 
courses

• SIAM W o rk in g  G rou p  o n  CSE E d u
c a tio n . This site begins with an excellen t 
definition o f com putational scie n ce  as a 
distinct discipline, d escribes the research 
areas in w hich computational science plays 
an important role, and discusses graduate 
curricula and programs in CSE (Computa­

­

A b o u t th e  a u th o r

Anna Keller Gold is head o f  the Science an d Engineering Library a t the University o f  California, San Diego, e-mail: agold@ 
ucsd.edu



C&RL News ■ February 2002 / 113

tional Science and Engineering). Access: 
http://www.siam. org/cse/report.htm.

• Partnership for Advanced Computa­
tional Infrastructure (PACI) Education, 
Outreach and Training. This extensive site 
is devoted to education, outreach, and train­
ing. It includes online lesson plans, courses, 
tutorials, and educational simulations. Access: 
http://www.eot.org/.

• Computational Science Education 
Project (CSEP). Aimed at advanced under­
graduates and higher-level students in science 
and engineering, this site includes an online 
textbook and tutorials for freely available 
networking and visualization software. Ac­
cess.-http://csepl.phy.ornl.gov/csep.html.

Hardware and software
Doing computational science requires exper­
tise in a scientific discipline, mathematical 
modeling, and knowledge of computer sci­
ence. A researcher also needs access to spe­
cialized hardware and software, from hard­
ware arrangements in clusters, like AppleSeed 
and Beowulf, to Cray-like supercomputers to 
enormous distributed “virtual” machines or 
computing “grids.”

Work on this hardware in turn commonly 
entails using the parallel computing algorithms 
that enable fast, high-volume processing of 
very large amounts of data, and software that 
allows scientists to develop models and simu­
lations and to visualize research results. To­
gether with the needed hardware, these com­
putational tools provide opportunities to or­
ganize very large amounts of data in ways 
that both express and invite interpretation and 
understanding.

• AppleSeed. AppleSeed is all about “per­
sonal parallel computing” on a cluster of com­
puters running Mac operating systems. Access: 
http://exodus.physics.ucla.edu/appleseed/ 
appleseed.html.

• Parallel Virtual Machine (PVM). Thor­
ough technical site for this free software pack­
age that allows a heterogeneous collection 
of Unix or NT computers (or both), connected 
by a network, to act as a single large parallel 
computer. Access: http://www.epm.ornl. 
gov/pvm/pvm_home. html.

• IEEE Task Force on  Cluster Comput­
ing. Lots of organizational information here, 
but dig deeper for excellent links to newslet­
ters, conferences, educational materials, e-

print repositories in cluster computing (click 
on “CC archive”), and other parallel comput­
ing information portals, such as Beowulf. A c­
cess: http://www.ieeetfcc.org/.

• Parallel COMputing Portal (PCOMP). 
A peer-rev iew ed  archive o f essen tial 
hyperlinks for high-performance parallel com­
puting. The site also includes lists of HPC 
newsletters and journals, meetings, tutorials, 
conferences, software, and benchmarks. Ac­
cess: http://www.npaci.edu/PCOMP/.

• Parallel Tools Consortium. This site 
brings together tool users, 
developers, and research­
ers from academia, gov­
ernment, and industry to 
improve the usability and 
availability of parallel 
tools. A ccess: http:// 
www.ptools.org/.

• Parascope. Hosted by IEEE, Parascope 
includes a comprehensive list of supercom­
puting and parallel computing centers, jour­
nals and conferences, HPC vendors, and 
federal agencies involved in HPC. Also lists 
the top 500 supercomputer sites and the 
“World’s Most Powerful Computing Sites.” Ac­
cess: http://computer.org/parascope/.

• T era Grid (D istributed Terascale 
Facility). A joint effort of supercomputing 
centers in Illinois and California, the Dis­
tributed Terascale Facility will offer more 
than 13-6 teraflops (trillions of calculations 
per second) of computing power and will 
manage and store more than 450 terabytes 
(trillion of bytes) of data. Access: http:// 
w w w .npaci.edu/teragrid/ and http:// 
www.teraarid.ora/.

• Terascale Computing System (TCS).
Nicknamed “Lemieux” (in honor of the Pitts­
burgh Penguins star), this research grid, ca­
pable of six teraflops per second, is funded 
by the National Science Foundation and 
housed at the Pittsburgh Supercomputing 
Center. A ccess: http://www.psc.edu/ma- 
chines/tcs/status/.

http://www.siam
http://www.eot.org/
http://csepl.phy.ornl.gov/csep.html
http://exodus.physics.ucla.edu/appleseed/
http://www.epm.ornl
http://www.ieeetfcc.org/
http://www.npaci.edu/PCOMP/
http://www.ptools.org/
http://computer.org/parascope/
http://www.npaci.edu/teragrid/
http://www.teraarid.ora/
http://www.psc.edu/ma-


114 /C& RL News ■ Feb ruary 2002

D iscip lin ary p o rtals and g a te w a y s
Portals in com p u tatio n al s c ie n c e , as in 
other endeavors, serve as gateways to in­
formation. In com putational science, “por­
tal” also may m ean an integrated, rem otely 
accessed  platform or “scientific w orkbench 
widely acce ssib le  through netw orking and 
optim ized for a particular set o f problem s 
or a problem -solving paradigm .”6 Portals 
are therefore focused  on a research do­
main or d iscip lin e and provide a place 
w here researchers can deposit, access, and 
manipulate data relevant to their work.

B iology a n d  m e d ic in e
•  B iology W o rk b en ch . From this site bi­

ologists can search many popular protein and 
nucleic acid sequence databases. Database 
searching is integrated with access to a wide 
variety o f analysis and modeling tools, all 
within a point and click interface. A ccess: 
http (//workbench, sdsc. edu/.

• B io m e d ica l In fo r m a tic s  R e s e a rc h  
N etw ork (BIRN). Originally the “Brain Im­
aging Research Network,” this huge national 
initiative has been broadened to encompass 
biomedical informatics generally. It will al­
low researchers nationwide to share high- 
resolution animal and human brain images 
to enable analysis and comparison at many 
different scales. A ccess: http://birn.ncrr.nih. 
gov/.

• C om p u tation al N eu roscien ce. This is 
a comprehensive, annotated information por­
tal maintained by Jim  Perlewitz. There are 
links to modeling and simulation software, 
major laboratories, researchers, conferences, 
education, and funding for theoretical neu­
robiology. A ccess: http://home.earthlink.net/ 
-perlewitz/.

• N ation al C en ter fo r B io te ch n o lo g y  
In fo rm a tio n  (NCBI). Since 1988, NCBI has 
been a crucial national resource for m olecu­
lar biology information, producing public da­
tabases, conducting research, and develop­
ing software tools for analyzing genome data. 
This site includes links to molecular and ge­
nomic databases, literature, books, software, 
and tutorials. A ccess: http://www.ncbi.nlm. 
nih.gov/.

• P ro te in  D ata B an k  (PD B ). This is the 
single worldwide repository for macromolecu- 
lar structure data, operated by University of 
C aliforn ia San D ieg o  and the R esearch

Collaboratory for Structural Bioinformatics. 
A ccess: http://www.rcsb.org/pdb/.

C hem istry
•  A ustralian C om putational C hem istry 

via th e  In te rn e t P ro je ct (ACCVIP). Aimed 
at developing educational modules in com­
putational chemistry for use in undergradu­
ate and postgraduate teaching, this joint ef­
fort by faculty at several Australian universi­
ties includes a list o f Web links to computa­
tional chemistry resources. A ccess: http:// 
www .chem.swin.edu.au/chem_ref. html.

• ChemViz. A chemistry visualization pro­
gram, ChemViz uses a Web interface to gen­
erate images o f atoms, molecules, and atomic 
orbitals. Resources are also available for teach­
ers to take advantage o f ChemViz in second­
ary sch oo ls. A ccess: http://chem viz.ncsa. 
uiuc.edu/.

• GAMESS: G en eral A tom ic an d  Mo­
le cu la r E le ctro n ic S tru ctu re System . This 
site supports computational research in quan­
tum chemistry. A ccess: http://gridport.npad. 
edu/GAMESS.

E n g in eerin g
•  C o m p u t a t i o n a l  F lu id  D y n a m ic s  

O nline. A comprehensive information por­
tal maintained since 1994 by Jonas Larsson, 
with links to academic sites, organizations, 
newsgroups, projects, software, hardware, 
jobs, and introductions to the field. A ccess: 
http://www.cfd-online.com/.

E n v iron m en t a n d  g e o s c ie n c e s
•  CCS Clim ate R e se a rch  C om m u n ity.

An information portal at the Oak Ridge Na­
tional Laboratory, this site consists o f links to 
research efforts such as the Parallel Climate 
Model. A ccess: http://www.ccs.ornl.gov/ 
climate.html.

Linguistics
• ACL NLP/CL U n iverse. An information 

portal o f the Association for Computational 
Linguistics on Natural Language Processing 
and Computational Linguistics, with links to 
people, conferences, academic departments, 
jobs, introductory materials, linguistic corpora,

http://birn.ncrr.nih
http://home.earthlink.net/
http://www.ncbi.nlm
http://www.rcsb.org/pdb/
http://chemviz.ncsa
http://gridport.npad
http://www.cfd-online.com/
http://www.ccs.ornl.gov/


C&RL News ■ February 2002 /115

and more. Access: http://perun.si.umich.edu/ 
~radev/u/db/acl/.

M athem atics
• Netlib. A repository of mathematical 

software, papers, and data­
bases relevant to computa­
tional mathematics, hosted 
by the University of Tennes­
see and Oak Ridge National 
Laboratories. Access: http://

www. netlib. org/ index, html.

Physics a n d  astronom y
• GriPhyN: Grid Physics Network. The

GriPhyN (Grid Physics 
Network) collaboration 
plans to implement the 
first P e ta b y te -s c a le 7 
computational environ­
ment for data intensive 
science in the 21st cen­
tury; it is funded by the 

National Science Foundation. Access: http:// 
www.griphyn.org/.

• Particle Physics Data Grid. A collabo­
ration o f U.S. federal laboratories and several 
U.S. universities, enabling a worldwide dis­
tributed computing model of current and fu­
ture high-energy and nuclear physics experi­
ments. Access: http://www.ppdg.net/.

• Digital Sky Survey. This site is an ef­
fort to federate data from multiple large-scale 
sky surveys to provide a perspective of the 
universe that is statistical and data-focused, 
in contrast to traditional work with individual 
stellar objects. A ccess: http://www.cacr. 
caltech.edu/SDA/digital_sky.html.

Who does computational science?
U.S. federal laboratories affiliated with the De­
partment of Energy have long had a critical 
role in developing and using high-performance 
computing capabilities. The National Science 
Foundation has also invested in large-scale 
partnerships that make supercomputing facili­
ties available for academic scientific research. 
Private industry, scholarly associations, and 
educational programs and university research 
institutes also have key roles in carrying out 
computational science, as do rare individuals 
like David and Gregory Chudnovsky, who built 
their computational mathematics hardware and 
software from scratch.8

Governm ent agencies
• P artnerships for Advanced Compu­

tational Infrastructure (PACI). Funded by 
the National Science Foundation, PACI is the 
umbrella under which two major national 
computational partnerships operate: NPACI 
and the Alliance. PACI partners develop, ap­
ply, and test the software, tools, and algo­
rithms to create a national grid of intercon­
nected, high-performance computing systems. 
Access: http://www.paci.org/.

• National P artn ersh ip  fo r Advanced 
C om putational In frastru ctu re (NPACI).
B ased  in San D iego at the San D iego 
Supercomputer Center (http://www.sdsc. 
edu), NPACI publishes an excellent newslet­
ter (Online), holds workshops, provides re­
search information, and develops resources 
developed to enable computational science. 
Access: http://www.npaci.edu/.

• T he A lliance (N ation al C om p uta­
tional Science Alliance). Based in Illinois 
at the National Center for Supercomputing 
Applications, the Alliance is a partnership of

m ore than 50 
academic, gov­
ern m en t, and 
business organi­
zatio n s. T h eir 
site features an 

excellent newsletter (Access') and educational 
and research events (including Web casts). 
Access: http://www.ncsa.uiuc.edu/.9

Federal agencies and research 
centers

• Federal National Laboratories. Many 
federal national laboratories operate signifi­
cant computational science programs. This site 
provides a comprehensive directory by labo­
ratory name to all U.S. federal labs. Access: 
http://www.federallabs.org/laboratories_ 
national.html.

• National Energy Research Scientific 
Computing Center. Funded by the Depart­
ment of Energy, and home of the “world’s larg­
est unclassified supercomputer,” this center 
supports research in astrophysics, climate re­
search, and materials science. News, technical

http://perun.si.umich.edu/
http://www.griphyn.org/
http://www.ppdg.net/
http://www.cacr
http://www.paci.org/
http://www.sdsc
http://www.npaci.edu/
http://www.ncsa.uiuc.edu/.9
http://www.federallabs.org/laboratories_


116 /  C&RL N ews ■ Feb ru a ry 2002

help, publications, and more. Access: http:// 
www.nersc.gov/.

• NASA A dvan ced  S u p ercom p u tin g Di­
v isio n  (NAS). Located at NASA Ames Re­
search Center, the mission o f NAS is to “de­
velop, demonstrate, and deliver innovative, 
distributed heterogeneous computing capa­
bilities to enable NASA projects and missions.” 
Also publishes G ridpoin ts magazine. A ccess: 
http://www.nas.nasa.gov/.

A ca d e m ic p ro g ram s, rese a rch  
ce n ters, and co n so rtia

• N o rth w e s t A llia n ce  f o r  C o m p u ta ­
tio n a l S cien ce an d  E n g in eerin g  (NACSE).
A coalition o f Pacific Northwest institutions 
and individuals that provides scientists, engi­
neers, and students with Web-based training 
materials and tools for learning about compu­
tational techniques and parallel programming. 
A ccess: http://www.nacse.org/.

• SUNY B ro c k p o r t’s Guide to  C om p u ­
ta t io n a l S c ie n c e  a n d  E n g in e e r in g  P r o ­
g ra m s a n d  Societies. A comprehensive list­
ing of degree-granting programs in the United 
States, Canada, and other nations, as well as 
professional societies active in computational 
research. A ccess: http://www.cps.brockport. 
edu/cps-links. html.

A ss o c ia tio n s an d  co n fere n ces
• S u p ercom pu tin g C on­

f e r e n c e . Billed  as “The In ­
tern atio n al C o n fe re n ce  for 
High P erform ance Comput­
ing and  C o m m u n ic a tio n ,” 
this a n n u al c o n f e r e n c e  is 
s p o n so re d  in part by IEEE 
an d  ACM. A c c e s s : http:// 
www.supercomp.org/.

• In tern atio n al C o n feren ce o n  C om pu­
ta tio n a l S c ie n c e  (IC C S). An international, 
m ultidisciplinary scientific com puting co n ­
fe re n ce  aim ed at bringing research ers and 
scientists to geth er with softw are d ev elop ­

ers and vendors. The n ext co n fe re n ce  will 
b e  held April 2002 in the N etherlands. A c ­
c e s s : http://w w w .science.uva.nl/events/ 
ICCS2002/.

Notes
1. SIAM Working Group on CSE Educa­

tion, “Graduate Education for Computational 
Science and Engineering,” http://www.siam. 
org/cse/ report.htm.

2. See advertisem ents for positions at 
C altech in the August 2001 issue o f C o m ­
m u n i c a t i o n s  o f  th e  ACM  and the Sep tem ­
b e r  2 0 0 1  is s u e  o f  P h y s i c s  T o d a y . “At 
present, a significant fractio n o f scientific 
research  at C altech relies on large-scale 
distributed com puting; scalab le algorithms 
and data structures; the record ing, han ­
dling, processing, and visualization o f large 
data sets; and the organization of, and a c ­
cess to, large d atabases. T h e se  and related 
e n d e a v o rs in a p p lie d  m ath em atics and 
com puter scien ce are recognized as an area 
o f research  in its ow n right: Com putational 
S cien ce  and Engineering (C S E ).”

3. George Johnson, “All Science is Com­
puter S c ie n c e ,” March 25, 2001, N ew  York 
Tim es. “…  as research  on so many fronts 
is b e co m in g  in creasin gly d ep en d e n t on 
com putation, all s cie n ce , it seem s, is b e ­
com ing com puter s c ie n c e .”

4. SIAM Working Group on CSE Educa­
tion, op cit.

5. The chair o f SUNY Brockport’s com ­
putational science and engineering depart­
ment, quoted by Florence Olsen, “Computa­
tional Science Spans Barriers B etw een Tradi­
tional Disciplines,” C h ro n ic le o f  H ig h er E d u ­
c a tio n , November 24, 2000.

6. http://www.computer.org/computer/ 
articles/einstein_1299_2.htm . See also Mary 
Thom as, “Com putational S cie n ce  Portals: 
T he SDSC Grid Portal Toolkit (G rid P o rt),” 
NPACI Parallel Computing Institute 2000.

7. A p e t a b y t e  is e q u a l  t o  1 , 0 2 4  
te ra b y te s.

8. “Mountains o f Pi,” N ew  Yorker, March
2, 1992.

9. Logos for the NCSA and the Alliance 
are reproduced with permission o f the Na­
tional Center for Supercomputing Applications 
(NCSA), http://www.ncsa.uiuc.edu/. Copy­
right 2002, University o f Illinois Board of 
Trustees. ■

http://www.nersc.gov/
http://www.nas.nasa.gov/
http://www.nacse.org/
http://www.cps.brockport
http://www.supercomp.org/
http://www.science.uva.nl/events/
http://www.siam
http://www.computer.org/computer/
http://www.ncsa.uiuc.edu/