scientific papers mentioning Tcl

Arjen Markus (12 june 2008) I have access to several online literature databases (yes, lucky me :)), one of them is ScienceDirect by Elsevier (I have no shares in that company, I just want to document where I got the information from). A search for articles mentioning "Tcl" in one way or another brings up a lot of titles. I have selected those that use "Tcl" in the sense that we like: Tool Command Language - you'd be surprised how many meanings these three letters have - total cooking loss, two component limit, T cell lines and transverse carpal ligament are but a few!

I did not go through the whole list, just the first 200 or so. Not all of them describe the use of Tcl in their work (some merely mention it). I selected only one by Clif Flynt and added two from beyond the first 200 that had familiar names. Here is the list:

GRID computing approach for multireservoir operating rules with uncertainty
Environmental Modelling & Software, In Press, Corrected Proof, Available online 24 December 2008
Andrea Sulis

Dimensionality reduction based on rough set theory: A review
Applied Soft Computing, Volume 9, Issue 1, January 2009, Pages 1-12
K. Thangavel, A. Pethalakshmi

Overset grid technology development at NASA Ames Research Center
Computers & Fluids, Volume 38, Issue 3, March 2009, Pages 496-503
William M. Chan

Optimal control in NMR spectroscopy: Numerical implementation in SIMPSON
Journal of Magnetic Resonance, In Press, Corrected Proof, Available online 8 December 2008
Zdenek Tosner, Thomas Vosegaard, Cindie Kehlet, Navin Khaneja, Steffen J. Glaser, Niels Chr. Nielsen

Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies
Computers & Geosciences, Volume 34, Issue 7, July 2008, Pages 738-753
Luca Pallozzi Lavorante, Hans Dirk Ebert

NMR experimental procedure for obtaining 3Q and 5QMAS spectra from the same multiplex SPAM acquisition
Comptes Rendus Chimie, Volume 11, Issues 4-5, April-May 2008, Pages 380-386
Redouane Hajjar, Yannick Millot, Pascal P. Man

An Automated Approach to NMR Data Handling for Compound Validation and Registration
Journal of the Association for Laboratory Automation, Volume 13, Issue 2, April 2008, Pages 73-78
Alvin C. Bach II, Walter W. Massefski, James F. Mattes

EMPIRE: Nuclear Reaction Model Code System for Data Evaluation
Nuclear Data Sheets, Volume 108, Issue 12, December 2007, Pages 2655-2715
M. Herman, R. Capote, B.V. Carlson, P. Oblozinský, M. Sin, A. Trkov, H. Wienke, V. Zerkin

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.
BMC Genomics. 2007 Aug 29;8(1):294.
Jean Muller, Mehlen A, Vetter G, Yatskou M, Muller A, Chalmel F, Poch O, Friederich E, Vallar L.

Novel Software Automated Testing System Based on J2EE
Tsinghua Science & Technology, Volume 12, Supplement 1, July 2007, Pages 51-56
Songwen Pei, Baifeng Wu, Kun Zhu, Qiang Yu

Visualization of large data sets by mixing Tcl and C++ interfaces to the VTK library
Computers & Structures, Volume 85, Issue 9, May 2007, Pages 536-552
Frédéric Magoulès, Roman Putanowicz

An intelligent NC program processor for CNC system of machine tool
Robotics and Computer-Integrated Manufacturing, Volume 23, Issue 2, April 2007, Pages 160-169
Yadong Liu, Xingui Guo, Wei Li, Kazuo Yamazaki, Keizo Kashihara, Makoto Fujishima

ESPResSo - an extensible simulation package for research on soft matter systems
Computer Physics Communications, Volume 174, Issue 9, 1 May 2006, Pages 704-727
H.J. Limbach, A. Arnold, B.A. Mann, C. Holm

Sequence and Comparative Genomic Analysis of Actin-related Proteins.
Molecular Biology Cell (2005).
Jean Muller, Oma, Y., Vallar, L., Friederich, E., Poch, O., and Winsor, B.

Interpretive OpenGL for computer graphics
Computers & Graphics, Volume 29, Issue 3, June 2005, Pages 331-339
Bo Chen, Harry H. Cheng

GEOSSAV: a simulation tool for subsurface applications
Computers & Geosciences, Volume 30, Issue 3, April 2004, Pages 221-238
Christian Regli, Lukas Rosenthaler, Peter Huggenberger

REDCAT: a residual dipolar coupling analysis tool
Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241
Homayoun Valafar, James H. Prestegard

Visualisation of 4-D colour and power Doppler data
Ultrasound in Medicine & Biology, Volume 29, Issue 12, December 2003, Pages 1735-1747
Mike G. Jones, Jacqueline A. Shipley, Teresa M. Robinson

Automated scientific software scripting with SWIG
Future Generation Computer Systems, Volume 19, Issue 5, July 2003, Pages 599-609
D.M. Beazley

Are Scripting Languages Any Good? A Validation of Perl, Python, Rexx, and Tcl against C, C++, and Java
Advances in Computers, Volume 57, 2003, Pages 205-270
Lutz Prechelt

Tcl/Tk Features
Tcl/Tk (Second Edition), 2003, Pages 1-17
Clif Flynt

Developing a Simple NMR Interface: WWNMR
Journal of the Association for Laboratory Automation, Volume 7, Issue 6, 1 December 2002, Pages 103-107
Alvin C. Bach II, David W. Cochran

EMXtalOrg: an EM tilt data organization and processing system
Ultramicroscopy, Volume 93, Issue 1, October 2002, Pages 11-17
Jason McDermott, Eric Barklis

The design and implementation of the Redland RDF application framework
Computer Networks, Volume 39, Issue 5, 5 August 2002, Pages 577-588
David Beckett

Experience with SAND-Tcl: A Scripting Tool for Spatial Databases
Journal of Visual Languages & Computing, Volume 13, Issue 2, April 2002, Pages 229-255
CLAUDIO ESPERANÇA, HANAN SAMET

Automation of a procedure to find the polynomial which best fits (?, c1, c2, T) data of electrolyte solutions by non-linear regression analysis using ® software
Computers & Chemistry, Volume 26, Issue 3, February 2002, Pages 253-264
E. Cortazar, A. Usobiaga, L. A. Fernández, A. de Diego, J. M. Madariaga

Specification and Visualization of Anisotropic Interaction Tensors in Polypeptides and Numerical Simulations in Biological Solid-State NMR
Journal of Magnetic Resonance, Volume 154, Issue 1, January 2002, Pages 28-45
Mads Bak, Robert Schultz, Thomas Vosegaard, Niels Chr. Nielsen

Transcriber: Development and use of a tool for assisting speech corpora production
Speech Communication, Volume 33, Issues 1-2, January 2001, Pages 5-22
Claude Barras, Edouard Geoffrois, Zhibiao Wu, Mark Liberman

Multi-level annotation in the Emu speech database management system
Speech Communication, Volume 33, Issues 1-2, January 2001, Pages 61-77
Steve Cassidy, Jonathan Harrington

SIMPSON: A General Simulation Program for Solid-State NMR Spectroscopy
Journal of Magnetic Resonance, Volume 147, Issue 2, December 2000, Pages 296-330
Mads Bak, Jimmy T. Rasmussen, Niels Chr. Nielsen

Multi-agent approach to the planning of power transmission expansion
Decision Support Systems, Volume 28, Issue 3, May 2000, Pages 279-290
Jerome Yen, Yonghe Yan, Javier Contreras, Pai-Chun Ma, Felix F. Wu

Facial reconstruction using 3-D computer graphics
Forensic Science International, Volume 108, Issue 2, 14 February 2000, Pages 81-95
P. Vanezis, M. Vanezis, G. McCombe, T. Niblett

A New Automated Molecular Modeling Method to Locate Coke and to Follow Its Growth Inside Zeolite: Application to the Coke Formed during the Transformation of Toluene on H-MFI
Journal of Catalysis, Volume 188, Issue 2, 10 December 1999, Pages 346-352

TCL/TK in a nutshell: A desktop quick reference : By Paul Raines and Jeff Tranter. O'Reilly, Sebastopol, CA. (1999). 440 pages. $24.95
Computers & Mathematics with Applications, Volume 38, Issues 5-6, September 1999, Page 255

Rough set extension of Tcl for data mining
Knowledge-Based Systems, Volume 11, Issues 3-4, 12 November 1998, Pages 249-253
G. Griffin, Z. Chen

Inter-site: a new tool for the simulation of spatially realistic population dynamics
Ecological Modelling, Volume 113, Issues 1-3, 2 November 1998, Pages 125-139
F. Oliver Gathmann, D. Dudley Williams

QVIEW: Software for Rapid Selection of Particles from Digital Electron Micrographs
Journal of Structural Biology, Volume 123, Issue 1, September 1998, Pages 17-21
Alexandre K. Shah, Phoebe L. Stewart

XML and the desperate Tel hacker
Computer Networks and ISDN Systems, Volume 30, Issues 1-7, April 1998, Pages 713-715
Steve Ball

Graphical user interfaces for numerical libraries
Journal of Computational and Applied Mathematics, Volume 82, Issues 1-2, 15 September 1997, Pages 351-366
Venkat V. S. S. Sastry

AM (16 january 2009) From a different literature database:

Title: Web Based Application for Registering Degree Projects 
Author(s): Fragidis L, Michailidis A, Mardiris V, et al.
Conference Information: 12th WSEAS International Conference on Computers, JUL 23-25, 2008 Heraklion, GREECE
Source: PROCEEDINGS OF THE 12TH WSEAS INTERNATIONAL CONFERENCE ON COMPUTERS , PTS 1-3 - NEW ASPECTS OF COMPUTERS  Book Series: Recent Advances in Computer Engineering   Pages: 567-571   Published: 2008 

Title: Design of Intelligent PID Controller Based on Adaptive Genetic Algorithm and Implementation of FPGA 
Author(s): Qu LG, Huang YR, Ling LY
Conference Information: 5th International Symposium on Neural Networks, SEP 24-28, 2008 Beijing, PEOPLES R CHINA
Source: ADVANCES IN NEURAL NETWORKS - ISNN 2008, PT 2, PROCEEDINGS  Book Series: LECTURE NOTES IN COMPUTER SCIENCE   Volume: 5264   Pages: 542-551   Published: 2008 

Title: G-JSIM - A GUI tool for Wireless Sensor Networks simulations under J-Sim 
Author(s): Neves PACS, Veiga IDC, Rodrigues JJPC
Conference Information: IEEE International Symposium on Consumer Electronics, APR 14-16, 2008 Vilamoura, PORTUGAL
Source: 2008 IEEE INTERNATIONAL SYMPOSIUM ON CONSUMER ELECTRONICS, VOLS 1 AND 2   Pages: 593-596   Published: 2008 

Title: Development of bridge rating applications using OpenSees and Tcl 
Author(s): Scott MH, Kidarsa A, Higgins C
Source: JOURNAL OF COMPUTING IN CIVIL ENGINEERING   Volume: 22   Issue: 4   Pages: 264-271   Published: JUL-AUG 2008 

Title: Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies 
Author(s): Lavorante LP, Ebert HD
Source: COMPUTERS & GEOSCIENCES   Volume: 34   Issue: 7   Pages: 738-753   Published: JUL 2008 

Title: A user-programmable link between data preparation and mask manufacturing equipment - art. no. 67304H 
Author(s): Zhang W, Davis G, Sahouria E, et al.
Conference Information: 27th Annual BACUS Symposium on Photomask Technology, SEP 18-21, 2007 Monterey, CA
Source: PHOTOMASK TECHNOLOGY 2007, PTS 1-3  Book Series: PROCEEDINGS OF THE SOCIETY OF PHOTO-OPTICAL INSTRUMENTATION ENGINEERS (SPIE)   Volume: 6730   Pages: H7304-H7304   Part: Part 1-3   Published: 2007 

AM (27 february 2009) Yet another database (warning: I have not checked for duplications):

The Implementation of Evolvable Hardware Closed Loop 
 
Author(s): Chu J (Chu Jie)1, Zhao Q (Zhao Qiang)1, Ding GL (Ding Guo-Liang)1, Yuan L (Yuan Liang)1  
Book Group Author(s): IEEE Computer Soc  
Source: INTERNATIONAL CONFERENCE ON INTELLIGENT COMPUTATION TECHNOLOGY AND AUTOMATION, VOL 2, PROCEEDINGS    Pages: 48-51    Published: 2008    


Web Based Application for Registering Degree Projects 

Author(s): Fragidis L (Fragidis, Leonidas)1, Michailidis A (Michailidis, Achilleas)1, Mardiris V (Mardiris, Vassilios)1, Chatzis V (Chatzis, Vassilios)1  
Editor(s): Mastorakis NE; Mladenov V; Bojkovic Z; Simian D; Kartalopoulos S; Varonides A  
Source: PROCEEDINGS OF THE 12TH WSEAS INTERNATIONAL CONFERENCE ON COMPUTERS , PTS 1-3 - NEW ASPECTS OF COMPUTERS    Book Series: Recent Advances in Computer Engineering    Pages: 567-571    Published: 2008    
Times Cited: 0     References: 8     Citation Map       
Conference Information: 12th WSEAS International Conference on Computers
Heraklion, GREECE, JUL 23-25, 2008
WSEAS  


Design of Intelligent PID Controller Based on Adaptive Genetic Algorithm and Implementation of FPGA 
 
Author(s): Qu LG (Qu, Liguo)1, Huang YR (Huang, Yourui)1, Ling LY (Ling, Liuyi)1  
Editor(s): Sun F; Zhang J; Tan W; Cao J; Yu W  
Source: ADVANCES IN NEURAL NETWORKS - ISNN 2008, PT 2, PROCEEDINGS   Book Series: LECTURE NOTES IN COMPUTER SCIENCE    Volume: 5264    Pages: 542-551    Published: 2008    
Times Cited: 0     References: 8     Citation Map       
Conference Information: 5th International Symposium on Neural Networks
Beijing, PEOPLES R CHINA, SEP 24-28, 2008  


G-JSIM - A GUI tool for Wireless Sensor Networks simulations under J-Sim 
 
Author(s): Neves PACS (Neves, Paulo A. C. S.)1, Veiga IDC (Veiga, Iuri D. C.), Rodrigues JJPC (Rodrigues, Joel J. P. C.)  
Book Group Author(s): IEEE  
Source: 2008 IEEE INTERNATIONAL SYMPOSIUM ON CONSUMER ELECTRONICS, VOLS 1 AND 2    Pages: 593-596    Published: 2008    
Times Cited: 0     References: 7     Citation Map       
Conference Information: IEEE International Symposium on Consumer Electronics
Vilamoura, PORTUGAL, APR 14-16, 2008
IEEE  


Development of bridge rating applications using OpenSees and Tcl 
 
Author(s): Scott MH (Scott, Michael H.)1, Kidarsa A (Kidarsa, Adrian)2, Higgins C (Higgins, Christopher)1  
Source: JOURNAL OF COMPUTING IN CIVIL ENGINEERING    Volume: 22    Issue: 4    Pages: 264-271    Published: JUL-AUG 2008    


Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies 
 
Author(s): Lavorante LP (Lavorante, Luca Pallozzi)1, Ebert HD (Ebert, Hans Dirk)2  
Source: COMPUTERS & GEOSCIENCES    Volume: 34    Issue: 7    Pages: 738-753    Published: JUL 2008    


A user-programmable link between data preparation and mask manufacturing equipment - art. no. 67304H 

Author(s): Zhang W (Zhang, Weldong)1, Davis G (Davis, Grant)1, Sahouria E (Sahouria, Emile)1, Schulze S (Schulze, Steffen), Saad M (Saad, Mohammed), Seyfarth A (Seyfarth, Arne), Poortinga E (Poortinga, Eric)  
Editor(s): Naber RJ  
Source: PHOTOMASK TECHNOLOGY 2007, PTS 1-3   Book Series: PROCEEDINGS OF THE SOCIETY OF PHOTO-OPTICAL INSTRUMENTATION ENGINEERS (SPIE)    Volume: 6730    Pages: H7304-H7304    Part: Part 1-3    Published: 2007    


ATTEST: A testing toolkit for validating software properties 

Author(s): Ren YJ (Ren, Yansong (Jennifer)), Chang FZ (Chang, Fangzhe)  
Book Group Author(s): IEEE  
Source: 2007 IEEE INTERNATIONAL CONFERENCE ON SOFTWARE MAINTENANCE   Book Series: PROCEEDINGS - IEEE INTERNATIONAL CONFERENCE ON SOFTWARE MAINTENANCE    Pages: 483-486    Published: 2007    

Actually, I have written also some papers that mainly involve the Ellogon (http://www.ellogon.org/ ) platform:

P. Fragkou, G. Petasis, A. Theodorakos, V. Karkaletsis, and C. D. Spyropoulos, 
“BOEMIE ontology-based text annotation tool”. 
In Proceedings of the 6th Language Resources and Evaluation Conference (LREC 2008), Marrakech (Morocco), May 28 – 30, 2008.

G. Petasis, P. Fragkou, A. Theodorakos, V. Karkaletsis, and C. D. Spyropoulos, 
“Segmenting HTML pages using visual and semantic information”. 
In Proceedings of the 4th Web as a Corpus Workshop (WAC2008), 6th Language Resources and Evaluation Conference (LREC 2008), Marrakech (Morocco), June 1, 2008.

D. Spiliotopoulos, G. Petasis, and G. Kouroupetroglou, 
“Prosodically Enriched Text Annotation for High Quality Speech Synthesis”. 
In Proceedings of the 10th International Conference on Speech and Computer (SPECOM-2005), pp. 313 – 316, Patras, Greece, 17 – 19 October, 2005.

G. Petasis, V. Karkaletsis, C. Grover, B. Hachey, M. T. Pazienza, M. Vindigni, J. Coch: 
“Adaptive, Multilingual Named Entity Recognition in Web Pages”. 
In Proceedings of the 16th European Conference on Artificial Intelligence (ECAI 2004), pp. 1073 – 1074, Valencia, Spain, August 22 – 27, 2004.

G. Petasis, V. Karkaletsis, D. Farmakiotou, I. Androutsopoulos, and C.D. Spyropoulos. 
“A Greek Morphological Lexicon and its Exploitation by Natural Language Processing Applications”. 
In Lecture Notes on Computer Science (LNCS), vol. 2563, 
"Advances in Informatics - Post-proceedings of the 8th Panhellenic Conference in Informatics", 
Springer Verlag, pp. 401 – 419, 2003. (http://www.springerlink.com/content/hcdjrlvj5nlybf5c/  )

G. Petasis, V. Karkaletsis, G. Paliouras and C. D. Spyropoulos, 
“Using the Ellogon Natural Language Engineering Infrastructure”. 
In Proceedings of the Workshop on Balkan Language Resources and Tools, 1st Balkan Conference in Informatics (BCI’2003), Thessaloniki, Greece, November 21, 2003. (http://www.iit.demokritos.gr/skel/bci03_workshop/papers/SESSION5_2-23_Petasis.pdf )

G. Petasis, V. Karkaletsis, and C. D. Spyropoulos, 
“Cross-lingual Information Extraction from Web pages: the use of a general-purpose Text Engineering Platform”. 
In Proceedings of the 4th International Conference on Recent Advances in Natural Language Processing (RANLP 2003), Borovets, Bulgaria, pp 381 – 388, September 10 – 12, 2003.

G. Petasis, V. Karkaletsis, G. Paliouras, I. Androutsopoulos and C. D. Spyropoulos, 
“Ellogon: A New Text Engineering Platform”. 
In Proceedings of the 3rd International Conference on Language Resources and Evaluation (LREC 2002), Las Palmas, Canary Islands, Spain, vol. I, pp. 72 – 78, May 2002.

At the risk of a bit of self-citation, here are a few more in the physics/chemistry literature, with a boring assortment of authors and venues. The last one has been cited well over 500 times at last look.

B.H. Toby, "CMPR - a powder diffraction toolkit". Journal of Applied Crystallography. 38(6): p. 1040-1 (2005).

B.H. Toby, "Inspecting Rietveld Fits from pdCIF: pdCIFplot". Journal of Applied Crystallography. 36(5): p. 1285-7 (2003).

B.H. Toby, "EXPGUI, a Graphical User Interface for GSAS". Journal of Applied Crystallography. 34: p. 210-3 (2001).

Papers that could mention Tcl, but don't

as nominated by author (or other person with good insight).

 Daniel Andrén, Lars Hellström and Klas Markström:
 On the complexity of matrix reduction over finite fields,
 Advances in Applied Mathematics, Vol. 39, no. 4 (2007), 428-452.
 http://dx.doi.org/10.1016/j.aam.2006.08.008

The last cases in the large computational study mentioned was done with a massively parallelized C program, but about half of the cases were first solved using a Tcl program, and even in the end it was the Tcl program that constructed input data for the C program.


AM (13 august 2009) Here are some other ones:

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer
Computer Methods and Programs in Biomedicine, Volume 95, Issue 2, August 2009, Pages 146-157
Don C. Bigler, Yaman Aksu, David J. Miller, Qing X. Yang

GRID computing approach for multireservoir operating rules with uncertainty
Environmental Modelling & Software, Volume 24, Issue 7, July 2009, Pages 859-864
Andrea Sulis

AM (11 june 2010) And some more (some only mention Tcl in connection to other work):

Detection system based on a novel large area hybrid detector
Microelectronics Journal, In Press, Corrected Proof, Available online 30 May 2010
A. Nascetti, P. Valerio, D. Caputo, G. de Cesare

A DSL toolkit for deferring architectural decisions in DSL-based software design
Information and Software Technology, Volume 52, Issue 7, July 2010, Pages 733-748
Uwe Zdun

Enforcing Security in Semantics Driven Policy Based Networks
Computer Standards & Interfaces, In Press, Accepted Manuscript, Available online 8 April 2010
Palanivel Kodeswaran, Sethuram Balaji Kodeswaran, Anupam Joshi, Tim Finin

Practical application of bioinformatics by the multidisciplinary VIZIER consortium
Antiviral Research, In Press, Corrected Proof, Available online 11 February 2010
Alexander E. Gorbalenya, Philippe Lieutaud, Mark R. Harris, Bruno Coutard, Bruno Canard, Gerard J. Kleywegt, Alexander A. Kravchenko, Dmitry V. Samborskiy, Igor A. Sidorov, Andrey M. Leontovich, T. Alwyn Jones

Quantum circuit’s reliability assessment with VHDL-based simulated fault injection
Microelectronics Reliability, Volume 50, Issue 2, February 2010, Pages 304-311
Oana Boncalo, Alexandru Amăricăi, Mihai Udrescu, Mircea Vlăduţiu

Mechanical Coupling in Myosin V: A Simulation Study
Journal of Molecular Biology, Volume 395, Issue 4, 29 January 2010, Pages 815-833
Victor Ovchinnikov, Bernhardt L. Trout, Martin Karplus

Routing exploiting multiple heterogeneous wireless interfaces: A TCP performance study
Computer Communications, Volume 33, Issue 1, 15 January 2010, Pages 23-34
Wonyong Yoon, Nitin Vaidya

Towards a web-based progressive handwriting recognition environment for mathematical problem solving
Expert Systems with Applications, Volume 37, Issue 1, January 2010, Pages 886-893
Ba-Quy Vuong, Yulan He, Siu Cheung Hui

AM (22 september 2010) I should not forget my own paper:

A.A. Markus, W.M.G. Courage and M.C.L.M. van Mierlo
A computational framework for flood risk assessment in the Netherlands
Scientific Programming, volume 18, number 2, 2010, pp. 93-105

nscerqueira (Sep 2010)

Cerqueira, N. M. F. S. A., Ribeiro, J., Fernandes, P. A. and Ramos, M. J. , 
VsLab—An implementation for virtual high-throughput screening using AutoDock and VMD. 
International Journal of Quantum Chemistry, n/a. doi: 10.1002/qua.22738

EF I'm terribly sorry just to add a link here, but I've written a number of papers mentioning Tcl , most of them are about scripting and virtual environments.

stevel Don't be sorry, it's perfectly appropriate and appreciated.

AM Exactly, one of the reasons for a page like this. However, some of the links turned up a 404 error.


AM (6 may 2013) Just came across this one:

Tool development based on FAST for performing design optimization of offshore wind turbines: FASTLognoter
Renewable Energy, Volume 55, July 2013, Pages 69-78
José E. Gutierrez, Blas Zamora, Julio García, María R. Peyrau