Journal of Structural Biology 125, 246–252 (1999)Article ID jsbi.1998.4079, available online at http://www.idealibrary.com on

The Electron Microscopy Outreach Program: A Web-Based Resourcefor Research and Education

Gina E. Sosinsky,*,† Timothy S. Baker,‡ Galen Hand,* and Mark H. Ellisman*,†

*Department of Neurosciences, and †San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive,La Jolla, California 92093-0608; and ‡Department of Biological Sciences, Lilly Hall of Life Sciences, Purdue University,

West Lafayette, Indiana 47907-1392

Received October 30, 1998, and in revised form December 22, 1998

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We have developed a centralized World Wide WebWWW)-based environment that serves as a resourcef software tools and expertise for biological elec-ron microscopy. A major focus is molecular electronicroscopy, but the site also includes information

nd links on structural biology at all levels of resolu-ion. This site serves to help integrate or link struc-ural biology techniques in accordance with usereeds. The WWW site, called the Electron Micros-opy (EM) Outreach Program (URL: http://em-utreach.sdsc.edu), provides scientists with compu-ational and educational tools for their research anddification. In particular, we have set up a centralizedesource containing course notes, references, and linkso image analysis and three-dimensional reconstruc-ion software for investigators wanting to learn aboutM techniques either within or outside of theirelds of expertise. r 1999 Academic Press

INTRODUCTION

Approaches for exploration of biological structuresith modern three-dimensional microscopy tech-iques are expanding rapidly. These technologicaldvances impact not only the imaging of structures,ut also the computational reconstruction methodsor calculating three-dimensional structures. At oneevel of resolution, the computational techniquessed to investigate the three-dimensional structuref macromolecular complexes, organelles, or cellsnclude crystallographic reconstruction, helical recon-truction, icosahedral reconstruction, single-particleeconstruction, electron tomography, and serial sec-ion reconstruction. At lower levels of resolution, aombination of computational and light microscopyechniques (including deconvolution methods in com-ination with wide-field, multiphoton, or confocalicroscopy) provides information on the cellular

rganization of specifically targeted molecules. Three-imensional electron microscopic (EM) techniques

ave been particularly useful for determining struc- N

246047-8477/99 $30.00opyright r 1999 by Academic Pressll rights of reproduction in any form reserved.

ures that are too small for light microscopy or too largeor NMR or X-ray techniques or in cases where crystalsre not available or possess only limited order.Advances in microscopes and associated computa-

ional capabilities have been substantial over theast few years and have occurred in all aspects of 3Deconstruction, including (1) image acquisition, (2)mage processing and analysis, (3) 3D visualizationnd presentation, and (4) image or three-dimen-ional structure interpretation (cf. Carragher and Smith,996, Journal of Structural Biology issue on Softwareor Microscopy, for a more complete treatise on softwarevailable for molecular and macromolecular micros-opy). These approaches are being communicated andhared with other structural biologists. Each structuraliological technique provides unique or complementarytructural information. Merging of data from differenttructural disciplines has provided new information atifferent levels of molecular or cellular organization (seehe review by Baker and Johnson, 1996, for a morextensive list of references to combining EM and x-raytructures; Stewart et al., 1997; Hoh et al., 1993; Yip etl., 1998; Hanein et al., 1998, Wriggers et al., 1998, 1999,nd other papers in this issue). There are exciting newechnologies for sharing microscopes, data, and analysisia the World Wide Web (WWW) (Ellisman et al., 1998;adida-Hassan, 1998, 1999; Wolf et al., 1998; Henri etl., 1997; Kisseberth et al., 1998; Zaluzec, 1998. Here wentroduce the Electron Microscopy (EM) Outreach Pro-ram, a Web-based resource integrated for bothesearch and education in electron microscopy. Thus,he site provides basic and advanced information onlectron microscopic computational techniques, ac-ess to software tools for computation and visualiza-ion, and access to computational resources avail-ble through the San Diego Supercomputer Center.

THE ELECTRON MICROSCOPY OUTREACHPROGRAM: RATIONALE AND IMPLEMENTATION

The EM Outreach Program is a joint project of the

ational Center for Microscopy and Imaging Re-

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247EM OUTREACH PROGRAM FOR RESEARCH/EDUCATION VIA THE WWW

earch (NCMIR, an NIH National Research Re-ource), the San Diego Supercomputer CenterSDSC), the National Partnership forAdvanced Com-utational Infrastructure (NPACI), and the Nationaliomedical Computational Resource (NBCR, an NIHational Research Resource). The EM Outreacheb site is accessible through the research Web page

f the SDSC, where it is listed with other NPACIiological thrust areas such as crystallography, mo-ecular biology, ecology, and neurosciences. Underhe National Science Foundation funded NPACI,DSC supports a partnership involving researchroups at 46 institutions throughout the Unitedtates focused on developing and disseminatingdvanced methods for computation, in many scien-ific areas, including structural biology. Integratinghe EM Outreach Program with NPACI researchrovides maximum exposure to scientists from otherisciplines accessing the general tools at SDSC. Ouroal is to produce and promote a centralized resourcehrough NCMIR and NPACI/SDSC. This is espe-ially important is light of the recent award of therotein Data Bank, the depository of high-resolutionrotein structures, to a consortium of three institu-ions, of which SDSC is one (Rutgers and the Na-ional Institutes of Standards are the two others; seeditorial, 1998, in Nature Structural Biology).Figure 1 shows the main menu page for the EMutreach Program. We have included links to data-ase resources such as the multidimensional imageata base (BioImage Project, Marabini et al., 1996),he Protein Data Bank (PDB), the Human Brainroject, sequence data bases, or other Web-basedesource sites. The Outreach Page also containsinks to professional organizations, educational Webites, and other research resources whose focus isither electron microscopy or structural biology.The EM Outreach Program is divided into two

ections: (1) a resource for educational tools and (2) aesource for software tools. The Web site contains aearch engine that acts as a glossary for the HTMLocuments as well as up- and down-links within eachection. The site is open to the general public.

1) Resource for Education Tools

The EM Outreach Program Home Page Web URLontains a link to an EM Web Course. This is aomprehensive ‘‘Web textbook’’ about transmissionlectron microscopy written in the HTML language.ur original source materials were lecture notes

rom a course taught by one of us (T.S.B.) for morehan 10 years. The notes are extensive and containables and figures obtained from published materialssee Fig. 2 for an example). The course is divided intohree sections: ‘‘The Microscope’’ (optics and physical

rinciples of transmission electron microscopy; com- n

arisons to light microscopy), ‘‘The Specimen’’ (meth-ds of biological specimen preparation for transmis-ion electron microscopy, e.g., negative staining,rozen-hydrated preparation, freeze-fracture, thin-ection preparation), and ‘‘The Image’’ (methods ofmage analysis and three-dimensional reconstruc-ion). These Web pages are accessible through aentral table of contents and contain links to otherppropriate sections and references (Fig. 3).

2) Resource for Software Tools

The EM Outreach Program also contains Webocuments with links to software tools listed on aage entitled Biological Microscopy Software (Fig. 4).

user can use the EM Outreach Program Homeage Web URL to search for software tools thatould be applicable to his/her research. A user cantilize this software in two ways, depending on thearticular program and their local computer re-ources. If the desired programs require particularesources, such as a parallel computing environmentor electron tomographic reconstruction, the useran run such software on computers at the SDSCacility. In this instance, the user will find a general-zed description of the programs and a URL on howo use the SDSC facility and a transparent interfaceo this utility. If the desired program runs on ‘‘ordi-ary’’ computers, the user can download softwareirectly to a local computer such as a Silicon Graph-cs Inc., Sun, or Digital Equipment workstation or aersonal computer. With this option, the user ac-esses descriptions of the programs and their func-ions and the URL needed to download the software.n particular, we are currently targeting softwarehat permits data from complementary techniques toe merged and analyzed (e.g., EM and x-ray or EMnd light microscopy). In addition to locating exist-ng software that the authors will allow us to distrib-te, we will take advantage of all appropriate soft-are advances made by NPACI, SDSC, or NCMIRnd distribute these via links in the EM Outreachoftware Web page. At present, links to SDSC compu-ational resources are the only links listed. Weelcome any additional listings on the EM Outreachrogram for Web sites that provide access to otherational or international computational resourceselated to biological microscopy. Of the softwareisted on the Biological Microscopy Software Page,nly the Parallel Tomography programs are cur-ently available on the high-performance parallelrocessing supercomputers at SDSC (and else-here). Researchers interested in using these re-

ources should contact Mark Ellisman at NCMIRmark@ncmir.ucsd.edu, or one of the other contactsoted on the NCMIR Web Pages, http://www-

cmir.ucsd.edu).

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248 SOSINSKY ET AL.

FIG. 1. Main menu of Web page to EM Outreach Program. Thnd to microscopy software. Also included on this page are linksesearch resources, and a search engine for finding topics within thf contents page of the Web course. Note: The figures presented ingures and text.

is page contains an overview of the project with links to the Web Courseto other structural biology organizations, databases, educational sites,e Web pages. A user can also access the search engine through the tablethis paper are in black and white; however, the Web pages contain color

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249EM OUTREACH PROGRAM FOR RESEARCH/EDUCATION VIA THE WWW

FIG. 2. Sample page of course contents. The page shown here is from the section entitled ‘‘I.A. Principles of the Transmission Electron

icroscope (TEM).’’

250 SOSINSKY ET AL.

FIG. 3. Table of contents of Web Course. This Web page contains an overview of the course contents and links to these sections.

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251EM OUTREACH PROGRAM FOR RESEARCH/EDUCATION VIA THE WWW

FIG. 4. Biological microscopy software Web page. This page contains short descriptions and links to software sites. The software isategorized by application.

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ACCESSIBILITY, DISTRIBUTION, ANDINCORPORATION OF NEW RESEARCH TOOLS

The EM Outreach Program has been accessiblehrough the World Wide Web at its public address,ttp://em-outreach.sdsc.edu, since January 1998. It

s available to anyone with an Internet browser suchs Netscape Navigator or Microsoft Explorer. Re-uests for posting links to software materials andther Web sites as well as any questions about theroject can be made by e-mail to Gina Sosinsky atsosinsky@ucsd.edu. Any suggestions or commentshat would expand the scope of this project, such asser group postings, are encouraged and appreci-ted.

FUTURE PLANS

We are developing tutorials, documentation, andample data to aid investigators in understandingnd utilizing these software programs. Some of theoftware tools listed already have good documenta-ion as part of their current release. Copyrightermissions for images for ‘‘version 1’’ of the Webourse will be obtained within a reasonable timerame (e.g., publication of this issue) or will beeplaced by similar figures without copyright restric-ions. A second edition of the Web course will incorpo-ate animations and advanced Web technology. Ex-mples of advanced Web technology includenteractive graphics, the use of JAVA applets forpecific applications, and virtual reality modelinganguage (VRML). VRML is a standard language forescribing interactive 3-D objects and virtual worldsor transmission across the Internet. VRML adds theext level of interaction after HTML providing struc-ured graphics, three-dimensional representations,nd animations. See http://www.sdsc.edu/vrml forurther details and examples. The improved Webourse will include exercises and animations that golong with the textual material and links to biblio-raphic databases. We will include links in the imagenalysis section about appropriate software andhere to access these packages or programs. We willlso solicit sections from leading researchers onther types of biological microscopic techniques, e.g.,mmunocytochemistry, confocal microscopy, and scan-ing probe microscopies (SPM/AFM), which willxpand the information already present in the course.

The EM Outreach Program project was initiated with fundsrom the National Science Foundation as part of the Computa-ional Biology support for the San Diego Supercomputer Center.he continuation and further development of this project are partf the directive of the NCMIR (http://www-ncmir.ucsd.edu) andre supported by NIH Grant RR04050 to Mark H. Ellisman.evelopment and maintenance of this Web site and related

nfrastructure are provided by NIH Grant RR08605 (NBCR,ttp://www.sdsc.edu/NBCR) and NSF GrantASC 97-5249 (NPACI,

ttp://www.npaci.edu). T.S.B. was supported by NIH Grant

M33050. G.E.S. was supported by NSF Grant MCB-9728338.e thank Dr. Maryann Martone and Steve Young for comments on

he manuscript; Adam Lathers for help with the search enginend formatting of some of the Web documents; and Millicentturgeon for help in organizing the Web-based course notes. Weedicate this paper to Dr. Steve Young.

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