About the journal Instructions for authors Publication notes Legal stuff SimTK.org Simbios Center

Volume 1-4	Reserved
Volume 5 (2005)
Article 5(1)	SimTK and its users		Sherman, M.A.
Article 5(2)	Simulation of biological structures with SimTK: definitions, scope, and requirements		Sherman, M.A.	Supporting Material
Article 5(3)	PREPRINT:The SimTK Framework for physics-based simulation of biological structures: preliminary design		Sherman, Middleton, Schmidt, Paik, Blemker, Habib, Anderson, Delp, Altman
Article 5(4)	Getting started with SubVersion (migrating from CVS to SVN)		Anderson, F.C.

About the Journal

The SimTK Engineering Journal is an internal, online, lightly peer-reviewed publication designed to serve the needs of SimTK software developers and other contributors for referenceable archival storage. Its primary purpose is to provide an archival chronological record of SimTK design, specification, and highly technical implementation documents suitable for referencing from within SimTK code. This allows programmers to reference drawings, pictures, equations, and supplementary media and also makes the documentation accessible to a wider audience. Publication in this internal record is not intended to preclude later publication in a scientific conference or scholarly journal, and previously published material may be republished here for convenient access.

SimTK was initiated as part of the NIH National Center for Biomedical Computation at Stanford, the National Center for Physics-Based Simulation of Biological Structures (Simbios). Information on the National Centers for Biomedical Computing can be obtained from here. Funding was provided through NIH Grant U54 GM072970.

Editor Michael A. Sherman Dept. of Bioengineering Stanford University James H. Clark Center, S241 318 Campus Drive West Stanford, CA 94305-5448 msherman@stanford.edu +1 (650) 725-6535

Associate editors Frank C. Anderson, Ph.D. Christopher M. Bruns, Ph.D. Ayman W. Habib, Ph.D. Bryan C. Keller, M.D. Jack L. Middleton

Senior advisors Russ B. Altman, M.D., Ph.D. Scott L. Delp, Ph.D. Jeanette P. Schmidt, Ph.D. David S. Paik, Ph.D.

Instructions for authors

The purpose of this journal is to encourage documentation and communication, so the submission process is intended to be friendly. You are encouraged to submit documents in whatever format you like; the main article will be converted to pdf and any supplementary material will be saved as-is. Submission of any material relevant to SimTK’s development is welcome. This includes pre-grant planning work, philosophy, design, requirements, specification, development, testing, results produced, white papers, unresolved issues, etc. It is not even necessary for articles to be complete or self-contained. For example, if you want an archival place for a hand-drawn diagram you can put that here too and then reference it from your code. Together we will pick a few appropriate reviewers, with the point being to catch errors or omissions that can be corrected prior to publication, not to prevent publication. Please email questions or materials directly to the Editor or call +1 (650) 725-6535 to discuss.

Publication notes

Each article is published in pdf format and may be accompanied by supplementary material in any format. Use of color is encouraged. Once published, participants may rely on the content and formatting of articles to remain unchanged, except that the cover page may be modified to include forward references to errata, revisions, follow-ons, or replacements which are published as separate articles. Articles are designated by a Volume#(Article#) pair. Although the initial volume was 2005, it is volume number 5; lower volume numbers are reserved for publishing older material of relevance to SimTK. Each article is considered an issue within its volume, so a typical reference looks like “SimTK Engr. J. 6(3):1-9, 2006” which would be the third article in volume 6. The SimTK Engineering Journal is published to journal.SimTK.org.

Trademarks and copyright

SimTK and Simbios are trademarks of Stanford University. Articles and supplementary materials are Copyright ©2005 Stanford University.