Open Source Tools, mostly Linux based, are discussed with reference to current research activities in the areas of modeling, simulation and design. Broader application, not just in Mechanical Engineering (author's basic field of study), is exhibited with the help of examples of reputed research publications. The open source software, available over the Internet, to solve the relevant research problems like numerical computation, data visualization, text processing and script based automation are enumerated.

1. Some examples of Open Source
computational tools for researchers
By
Ashish Sharma, PhD
ashishsharma71@gmail.com
http://teachingmodelingsimulation.blogspot.in/

2. Abstract
Open Source Tools, mostly Linux based, are
discussed with reference to current research
activities in the areas of modeling, simulation and
design. Broader application, not just in
Mechanical Engineering, is exhibited with the help
of examples of reputed research publications. The
open source software, available over the Internet,
to solve the relevant research problems like
numerical computation, data visualization, text
processing and script based automation are
enumerated.

3. Open Source [1]

“Open Source Software (OSS) is a computer
software with its source code made available
with a license in which the copyright holder
provides the rights to study, change and
distribute the software to anyone and for any
purpose“

A world-wide collaborative development
environment

Available for download from servers from
government organizations, universities,
dedicated organizations etc.

4. Open Source (contd.)

Every s/w is a store-house of years of
dedicated research of countless scholars – it
oughts to be available to all researchers, rich or
poor

For example – linear algebra, computational
linguistics, computational biology, cryptography
etc.

The Open Source phenomenon seems to be in
line with this basic idea

Every new and worthy idea is being
continuously included

5. Computation – deciphering MATH!!
[2]

God used beautiful mathematics in creating the
world - Paul Dirac

No employment can be managed without
arithmetic, no mechanical invention without
geometry - Benjamin Franklin

Where there is matter, there is geometry -
Johannes Kepler

An equation means nothing to me unless it
expresses a thought of God - Srinivasa
Ramanujan [3]

6. Linear Algebra

GSL – GNU Scientific Library

Scilab – a MATLAB substitute

GNU Octave – a MATLAB clone

GMP - GNU Multi-Precision Library is a library
for doing arbitrary-precision arithmetic

JAMA - a numerical linear algebra toolkit for
the Java programming language

SciPy, a large library of scientific tools. Includes
NumPy

7. Linear Algebra – research examples

Linear Fresnel Collector Receiver: Heat
Loss and Temperatures, Energy Procedia,
Volume 49, 2014, Pages 386-397, A.
Heimsath, F. Cuevas, A. Hofer, P. Nitz, W.J.
Platze

Ophidia: Toward Big Data Analytics for
eScience, Procedia Computer Science, Volume
18, 2013, Pages 2376-2385, S. Fiore, A.
D’Anca, C. Palazzo, I. Foster, D.N. Williams, G.
Aloisio

pH front tracking in the electrochemical

8. Linear Algebra – research
examples, contd.

Stability and vibration of thick laminated
composite sector plates, Ashish Sharma, H.B.
Sharda and Y. Nath, Journal of Sound and
Vibration , Vol. 287, 2005, pp. 1-23

Free vibration of moderately thick
antisymmetric laminated annular sector
plates with elastic edge constraints, Ashish
Sharma, International Journal of Mechanical
Sciences 83 (2014), pp. 124–132

A fully Bayesian approach to the parcel-based
detection-estimation of brain activity in fMRI,

9. Python

Fast & Easy to learn – huge volume of
learning resources, enthusiast ever eager to
help

Balance of High Level and Low Level
Programming

Available Libraries

Time-saver for repetitive tasks

Great for gluing together other programs
and tasks into a custom workflow

Popular, many researchers use it

10. Python – research examples

CMIstark: Python package for the Stark-
effect calculation and symmetry
classification of linear, symmetric and
asymmetric top wavefunctions in dc electric
fields, Computer Physics Communications,
Volume 185, Issue 1, January 2014, Pages
339-349, Yuan-Pin Chang, Frank Filsinger,
Boris G. Sartakov, Jochen Küpper

Python scripting libraries for subsurface fluid
and heat flow simulations with TOUGH2 and
SHEMAT, Computers & Geosciences, Volume
43, June 2012, Pages 197-206, J. Florian

11. Python – research examples, contd.

Efficient multi-objective calibration of a
computationally intensive hydrologic model with
parallel computing software in Python,
Environmental Modelling & Software, Volume
46, August 2013, Pages 208-218. Xuesong
Zhang, Peter Beeson, Robert Link, David
Manowitz, Roberto C. Izaurralde, Ali Sadeghi,
Allison M. Thomson, Ritvik Sahajpal, Raghavan
Srinivasan, Jeffrey G. Arnold

FIDIMO — A free and open source GIS
based dispersal model for riverine fish,
Ecological Informatics, In Press, Corrected

12. Python – research examples, contd.

Parallel distributed computing using Python,
Advances in Water Resources, Volume 34,
Issue 9, September 2011, Pages 1124-1139,
Lisandro D. Dalcin, Rodrigo R. Paz, Pablo A.
Kler, Alejandro Cosimo

Algorithmic differentiation in Python with
AlgoPy, Journal of Computational Science,
Volume 4, Issue 5, September 2013, Pages
334-344, Sebastian F. Walter, Lutz Lehmann

Secure embedded system hardware design – A
flexible security and trust enhanced approach,

13. GNU Octave – for MATLAB tasks

GNU Octave is a high-level interpreted
language, primarily intended for numerical
computations

It provides capabilities for the numerical
solution of linear and nonlinear problems, and
for performing other numerical experiments

It also provides extensive graphics capabilities
for data visualization and manipulation

Octave is normally used through its interactive
command line interface, but it can also be used
to write non-interactive programs

14. GNU Octave – contd.

15. GNU Octave – research examples

A Covariance NMR Toolbox for MATLAB and
OCTAVE, Journal of Magnetic Resonance,
Volume 209, Issue 1, March 2011, Pages 75-
78, Timothy Short, Leigh Alzapiedi, Rafael
Brüschweiler, David Snyder

Markov analysis of redundant standby
safety systems under periodic surveillance
testing, Reliability Engineering & System
Safety, Volume 133, January 2015, Pages 48-
58 Mario Hellmich, Heinz-Peter Berg

16. GNU Octave – research examples,
contd.

Simulation Platform: A cloud-based online
simulation environmentOriginal Research
Article, Neural Networks, Volume 24, Issue 7,
September 2011, Pages 693-698, Tadashi
Yamazaki, Hidetoshi Ikeno, Yoshihiro Okumura,
Shunji Satoh, Yoshimi Kamiyama, Yutaka
Hirata, Keiichiro Inagaki, Akito Ishihara,
Takayuki Kannon, Shiro Usui

Parameter optimisation and uncertainty
assessment for large-scale streamflow
simulation with the LISFLOOD model,
Journal of Hydrology, Volume 332, Issues 3–

17. Open Source s/w in Social and
Behavioral Sciences

Open source software in teaching mathematics,
Procedia - Social and Behavioral Sciences,
Volume 15, 2011, Pages 769-771, I. Kusbeyzi,
A. Hacinliyan, O.O. Aybar

Roles of teachers in e-learning: How to
engage students & how to get free e-learning
and the future, Procedia - Social and
Behavioral Sciences, Volume 2, Issue 2,
2010, Pages 5775-5787, İlker Yengin, Dilek
Karahoca, Adem Karahoca, Ahmet Yücel

Peer Interactions in Computer-Supported

18. Open Source s/w in Environmental
Modelling

GRASS GIS: A multi-purpose open source GIS,
Environmental Modelling & Software, Volume
31, May 2012, Pages 124-130, Markus Neteler,
M. Hamish Bowman, Martin Landa, Markus
Metz

A GIS-based open source pre-processor for
georesources numerical modeling,
Environmental Modelling & Software,
Volume 62, December 2014, Pages 52-64, P.
Berry, S. Bonduá, V. Bortolotti, C. Cormio,
E.M. Vasinil


19. Open Source s/w in Computational
Linguistics

Lessons learnt from the deployment of a
semantic virtual research environment, Web
Semantics: Science, Services and Agents on
the World Wide Web, In Press, Accepted
Manuscript, Available online 23 August 2014,
Peter Edwards, Edoardo Pignotti, Chris Mellish,
Alan Eckhardt, Kapila Ponnamperuma, Thomas
Bouttaz, Lorna Philip, Kate Pangbourne, Gary
Polhill, Nick Gotts

An open-source toolkit for mining
Wikipedia, Artificial Intelligence, Volume 194,
January 2013, Pages 222-239, David Milne,

20. Open Source s/w in Mechatronics –
Open Source h/w!!!

E-training in mechatronics using innovative
remote laboratory, Mathematics and Computers
in Simulation, Volume 82, Issue 3, November
2011, Pages 508-516, A. Rojko, D. Hercog, K.
Jezernik

Commons-based peer production and
digital fabrication: The case of a RepRap-
based, Lego-built 3D printing-milling
machine, Telematics and Informatics,
Volume 31, Issue 3, August 2014, Pages 434-
443, Vasilis Kostakis, Marios Papachristou


21. LaTeX

A document preparation system [8]

Reputed publishers accepting LaTeX format:
– Elsevier
– IEEE
– ASCE
– ASME
– Association for Computing Machinery (ACM)
– American Chemical Society (ACS) Publications
– Etc.

22. References
[1] http://en.wikipedia.org/wiki/Open-
source_software
[2] google.co.in
[3]
http://todayinsci.com/R/Ramanujan_Srinivasa/R
amanujanSrinivasa-Quotations.htm
[4]
http://en.wikipedia.org/wiki/List_of_numerical_lib
raries

23. References
[5]
http://www.stat.washington.edu/~hoytak/_static/pap
[6] sciencedirect.com
[7] https://www.gnu.org/software/octave/
[8] www.latex-project.org/
[9]
http://blog.practicalsanskrit.com/2009/09/smile-
for-you-are-worth-it.html

24. "There is no syllable from which a mantra cannot
be made. There is no herb from which a
medicine cannot be made. There is no person
who is incapable. Who is rare is the one who
can organize."
Thanks!