Difference between revisions of "Citizen Science/Open Spectrophotometer Project/Documentation"

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==Spectrometric data format==
 
==Spectrometric data format==
 +
* JCAMP format:
 +
** [http://hackberry.trinity.edu/IJC/instructions/jcamp.html JCAMP format]
 +
** [http://wwwchem.uwimona.edu.jm/software/jcmpsum.html JCAMP DX format]
 +
** [http://wwwchem.uwimona.edu.jm/spectra/specindex.html JCAMP display applet]
 +
 
* XML/RDF based
 
* XML/RDF based
 +
** [http://dx.doi.org/10.1016/S1535-5535(04)00168-6 SpectroML Standard (2004)]
 +
** [http://www.jalajournal.com/article/S1535-5535(04)03276-9/abstract Documenting laboratory workflows using the Analytical Information Markup Language 2005]
 
* Data description:
 
* Data description:
 
** Spectral data (sampled)
 
** Spectral data (sampled)
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==Targeted biological samples==
 
==Targeted biological samples==
 +
 +
For our project, we aim to target one of the most accessible human bodily fluids:
 +
* '''Sweat'''
 +
** Still difficult to use as it is difficult to collect a quantity large enough
 +
** Reliable collection a problem too
 +
* '''Saliva'''
 +
** Few practical collection problems
 +
** [https://www.23andme.com 23andME]
 +
** Saliva Analysis is used to detect the level of hormones or drugs. But there is little a spectrophotometer can do to help (no correlation between a health issue and opacity, color or any such criterion).
 +
* '''Blood'''
 +
** Also Practical, although collection a bit harder
 +
** Anyone got a link to a 23andMe-like project?
 +
** Spectrophotometry may be of limited use, but of use nonetheless.
 +
** To know more about [[Citizen Science/Open Spectrophotometer Project/Documentation/Blood_Analysis | Blood Analysis]]
 +
* '''Urine'''
 +
** Also practical
 +
** Anyone got a link to a 23andMe-like project?
 +
** This is the bodily fluid for which spectrophotometry may be of most use.
 +
** To know more about [[Citizen Science/Open Spectrophotometer Project/Documentation/Urine_Analysis | Urine Analysis]]
 +
  
 +
 +
'''NB:''' There are also some internal bodily fluids (but they are not practical to use), including
 +
* cerebrospinal fluid surrounding the brain and the spinal cord
 +
* synovial fluid surrounding bone joints
 +
* intracellular fluid is the fluid inside cells
 +
* aqueous humour and vitreous humour the fluids in the eyeball.
 +
 +
A full (and very long) list of the human bodily fluids can be found on [http://en.wikipedia.org/wiki/Body_fluid Wikipedia]
  
 
==Open Dataset Repository design==
 
==Open Dataset Repository design==
 
* Web2.0 Service-like
 
* Web2.0 Service-like
 
* Open API
 
* Open API
 +
* Existing Spectroscopy Databases:
 +
** [http://www.lohninger.com/spectroscopy/dball.html Database listing]
 +
** UV-Vis:
 +
*** [http://chrom.tutms.tut.ac.jp/JINNO/DRUGDATA/00alphabet.html UV-Vis Spectra for Drugs]
 +
*** [http://www.science-softcon.de/uv-vis.htm UV Vis Softcon]
 +
 +
 +
* Papers:
 +
** [http://dx.doi.org/10.1016/S1381-141X(97)80007-X Development of in-house spectral-data manipulation programs following quality guides ]
 +
** ...
  
 
==Data visualisation==
 
==Data visualisation==
 +
* keywords from the 'Call for Projects'
 +
** [http://en.wikipedia.org/wiki/Rube_Goldberg_machine Rube Goldberg machines]
 +
** [http://en.wikipedia.org/wiki/Pataphysics Pataphysics]
 
* Processing-based
 
* Processing-based
 +
** [http://www.processing.org/exhibition/index.html Processing.org/exhibition/]
 +
* Tangible / physical / machines
 +
** [http://en.wikipedia.org/wiki/Fountain_(Duchamp) Duchamp's fountain]
 +
** [http://infosthetics.com/archives/2008/11/visible_sound_graph_sewing_machine.html data-sewing-machine]
  
 
==Data Analysis==
 
==Data Analysis==
 
* Data Analysis will play an important role in the second part of the project , that is the construction of the Web 2.0 Service
 
* Data Analysis will play an important role in the second part of the project , that is the construction of the Web 2.0 Service
* [[http://openwetware.org/wiki/Citizen_Science/Open_Spectrophotometer_Project/Documentation/Data_Analysis]]
+
* More on our apporach to data analysis can be found on [[Citizen Science/Open Spectrophotometer Project/Documentation/Data_Analysis | Data Analysis]]

Latest revision as of 05:30, 18 October 2011

Open Spectrophotometer Project

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Spectrophotometer design

  • Technology
    • LED-based
    • CCD detector
    • diffraction grating
  • Calibration
  • Computer interface

Spectrometric data format

Targeted biological samples

For our project, we aim to target one of the most accessible human bodily fluids:

  • Sweat
    • Still difficult to use as it is difficult to collect a quantity large enough
    • Reliable collection a problem too
  • Saliva
    • Few practical collection problems
    • 23andME
    • Saliva Analysis is used to detect the level of hormones or drugs. But there is little a spectrophotometer can do to help (no correlation between a health issue and opacity, color or any such criterion).
  • Blood
    • Also Practical, although collection a bit harder
    • Anyone got a link to a 23andMe-like project?
    • Spectrophotometry may be of limited use, but of use nonetheless.
    • To know more about Blood Analysis
  • Urine
    • Also practical
    • Anyone got a link to a 23andMe-like project?
    • This is the bodily fluid for which spectrophotometry may be of most use.
    • To know more about Urine Analysis


NB: There are also some internal bodily fluids (but they are not practical to use), including

  • cerebrospinal fluid surrounding the brain and the spinal cord
  • synovial fluid surrounding bone joints
  • intracellular fluid is the fluid inside cells
  • aqueous humour and vitreous humour the fluids in the eyeball.

A full (and very long) list of the human bodily fluids can be found on Wikipedia

Open Dataset Repository design


Data visualisation

Data Analysis

  • Data Analysis will play an important role in the second part of the project , that is the construction of the Web 2.0 Service
  • More on our apporach to data analysis can be found on Data Analysis