publication . Software Paper . Article . 2015

Scikit-spectra: Explorative Spectroscopy in Python

Adam Hughes; Zhaowen Liu; M. E. Reeves;
Open Access English
  • Published: 05 Jun 2015 Journal: Journal of Open Research Software (eissn: 2049-9647, Copyright policy)
  • Publisher: Ubiquity Press
Abstract
Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/
Subjects
free text keywords: biosensing; nanotechnology; software engineering; python programming, correlation spectroscopy; GUI; Python; IPython; Pandas; SciPy; scikits; spectroscopy; timeseries, correlation spectroscopy, GUI, Python, IPython, Pandas, SciPy, scikits, spectroscopy, timeseries, Computer software, QA76.75-76.765
26 references, page 1 of 2

1. Bohren, H 1983 Absorption and Scattering of Light by Small Particles, John Wiley & Sons, INC.

2. Ginsburg, A and Mirocha, J 2011 'PySpecKit: Python Spectroscopic Toolkit', Astrophysics Source Code Library, record ascl:1109.001 URL: http://adsabs. harvard.edu/abs/2011ascl.soft09001G

3. Gorsuch, R L 1983 Factor Analysis, 2nd edn, Lawrence Erlbaum Associats, Inc., Hillsdale, NJ.

4. Helmus, J and Jaroniec, C 2013 'Nmrglue: An open source Python package for the analysis of multidimensional NMR data', Journal of Biomolecular NMR 55(4), 355-367. URL: http://link.springer.com/article/10.1007/s10858-013-9718-x [OpenAIRE]

5. Hoyer, S 2015 'xray: N-D labeled arrays and datasets in Python'. URL: https://github.com/xray/xray

6. Hughes, A and Liu, Z 2014 'scikit-spectra: Tools for explorative spectroscopy'. URL: http://hugadams. github.io/scikit-spectra/

7. Jones, E, Oliphant, T and Peterson, P 2001 'Scipy: Open source scientific tools for Python'. URL: http:// www.scipy.org

8. Jordahl, K 2014 'GeoPandas: Python tools for geographic data'. URL: https://github.com/geopandas/ geopandas

9. McKinney, W 2010 Data Structures for Statistical Computing in Python, in S. van der Walt & J. Millman, eds, 'Proceedings of the 9th Python in Science Conference', pp. 51-56. URL: http://pandas.pydata.org/

10. Morita, S 2002 '2D Shige'. URL: https://sites.google. com/site/shigemorita/home/2dshige

11. Nájera, O 2014 'Sphinx-Gallery'. URL: https://github. com/sphinx-gallery/sphinx-gallery

12. Noda, I 2007 'Scaling techniques to enhance twodimensional correlation spectra', Journal of Molecular Structure 883-884, 216-227. URL: http://linkinghub. elsevier.com/retrieve/pii/S0022286007008411

13. Noda, I and Ozaki, Y 2004 Two-Dimensional Correlation Spectroscopy, Wiley.

14. Normand, E 2011 MIDAS 2010: Mid-Infrared Data Analysis Software 2010 A Matlab Package for 2D IR Spec-troscopy Analysis. URL: http://www.mathworks. com/matlabcentral/fileexchange/32384-midas-2010

15. Oliphant, T E 2007 'Python for Scientific Computing', Computing in Science & Engineering 9(90), 2007. URL: http://www.numpy.org/

26 references, page 1 of 2
Abstract
Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/
Subjects
free text keywords: biosensing; nanotechnology; software engineering; python programming, correlation spectroscopy; GUI; Python; IPython; Pandas; SciPy; scikits; spectroscopy; timeseries, correlation spectroscopy, GUI, Python, IPython, Pandas, SciPy, scikits, spectroscopy, timeseries, Computer software, QA76.75-76.765
26 references, page 1 of 2

1. Bohren, H 1983 Absorption and Scattering of Light by Small Particles, John Wiley & Sons, INC.

2. Ginsburg, A and Mirocha, J 2011 'PySpecKit: Python Spectroscopic Toolkit', Astrophysics Source Code Library, record ascl:1109.001 URL: http://adsabs. harvard.edu/abs/2011ascl.soft09001G

3. Gorsuch, R L 1983 Factor Analysis, 2nd edn, Lawrence Erlbaum Associats, Inc., Hillsdale, NJ.

4. Helmus, J and Jaroniec, C 2013 'Nmrglue: An open source Python package for the analysis of multidimensional NMR data', Journal of Biomolecular NMR 55(4), 355-367. URL: http://link.springer.com/article/10.1007/s10858-013-9718-x [OpenAIRE]

5. Hoyer, S 2015 'xray: N-D labeled arrays and datasets in Python'. URL: https://github.com/xray/xray

6. Hughes, A and Liu, Z 2014 'scikit-spectra: Tools for explorative spectroscopy'. URL: http://hugadams. github.io/scikit-spectra/

7. Jones, E, Oliphant, T and Peterson, P 2001 'Scipy: Open source scientific tools for Python'. URL: http:// www.scipy.org

8. Jordahl, K 2014 'GeoPandas: Python tools for geographic data'. URL: https://github.com/geopandas/ geopandas

9. McKinney, W 2010 Data Structures for Statistical Computing in Python, in S. van der Walt & J. Millman, eds, 'Proceedings of the 9th Python in Science Conference', pp. 51-56. URL: http://pandas.pydata.org/

10. Morita, S 2002 '2D Shige'. URL: https://sites.google. com/site/shigemorita/home/2dshige

11. Nájera, O 2014 'Sphinx-Gallery'. URL: https://github. com/sphinx-gallery/sphinx-gallery

12. Noda, I 2007 'Scaling techniques to enhance twodimensional correlation spectra', Journal of Molecular Structure 883-884, 216-227. URL: http://linkinghub. elsevier.com/retrieve/pii/S0022286007008411

13. Noda, I and Ozaki, Y 2004 Two-Dimensional Correlation Spectroscopy, Wiley.

14. Normand, E 2011 MIDAS 2010: Mid-Infrared Data Analysis Software 2010 A Matlab Package for 2D IR Spec-troscopy Analysis. URL: http://www.mathworks. com/matlabcentral/fileexchange/32384-midas-2010

15. Oliphant, T E 2007 'Python for Scientific Computing', Computing in Science & Engineering 9(90), 2007. URL: http://www.numpy.org/

26 references, page 1 of 2
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