XML toolbox from geodise

[Sonia Martins]

Hello,

I'm trying to use the XML-tool box downloaded from 
http://sourceforge.net/projects/octave-xmltools/ but I don't seem to be 
able to run the test scripts. I think there's something wrong with the 
way I'm trying to "link" the toolbox .m, .h, .cc files to Octave... I 
can't even successfully compile the xml_help.cc, xml_load.cc files using 
the mkoctfile method. The other problem is that this toolbox as far as I 
understand it uses some libraries from XERCES but can't figure out where 
these should be so that they're available to the xml-toolbox for Octave.
The documentation that comes with this toolbox is in .ZUML format, and 
after I unzipped I don't know how to read it...
Apart from this, if anyone is aware of a good XML solution to read in 
XML files in Octave as the one I'm sending attached to the email, please 
let me know...
Finally, as it is probably obvious by now, I'm new to Octave. I'm trying 
to move from Matlab so that everything is freeware from the software I 
use to run my simulations (iDynoMiCS) to the result analysis... but all 
the results are written in XML, hence the need for an XML reader that 
can extract information from the nodes, children, data...

Thank you very much for any time you can spare with my case :)
Sonia

--
Sónia Martins
PhD student
Centre for systems biology
School of Biosciences
University of Birmingham
Edgbaston, Birmingham B15 2TT
Email: address@hidden
Website: http://www.biosciences-labs.bham.ac.uk/kreftlab/
Phone: +44 121 414 48850


PhD Program in Computational Biology
Gulbenkian Institute
Email: address@hidden
Website: http://bc.igc.gulbenkian.pt/pdbc/

<idynomics>
 <simulation iterate="0" time="0.0" unit="hour">
<grid resolution="8.0" nI="65" nJ="65" nK="1"/>
<species name="HetEPS" 
header="family,genealogy,generation,birthday,biomass,inert,capsule,growthRate,volumeRate,locationX,locationY,locationZ,radius,totalRadius">
</species>
<species name="HetSwitchLag1" 
header="family,genealogy,generation,birthday,biomass,inert,capsule,growthRate,volumeRate,locationX,locationY,locationZ,radius,totalRadius,state,turnOn,turnOff,timeRequestTurnOn,timeRequestTurnOff">
2,0,0,0.0,11553.383780684591,0.0,0.0,0.0,0.0,2.070408765305566,343.29627808550407,0.0,1.7506064845649867,1.7506064845649867,0,0,0,0.0,0.0;
5,0,0,0.0,10190.39304506386,0.0,0.0,0.0,0.0,1.8432157976500614,179.1067716259571,0.0,1.644104433314138,1.644104433314138,0,0,0,0.0,0.0;
8,0,0,0.0,10709.62561851332,0.0,0.0,0.0,0.0,2.596947081248384,84.0865194725598,0.0,1.6854701965231058,1.6854701965231058,0,0,0,0.0,0.0;
4,0,0,0.0,9929.220599667437,0.0,0.0,0.0,0.0,2.3202882711737542,32.4706036704676,0.0,1.6228990747542473,1.6228990747542473,0,0,0,0.0,0.0;
1,0,0,0.0,9028.20964725846,0.0,0.0,0.0,0.0,2.277502444220676,461.48775758816373,0.0,1.5475145839801185,1.5475145839801185,0,0,0,0.0,0.0;
6,0,0,0.0,10937.195345151358,0.0,0.0,0.0,0.0,1.7177205466895495,489.68821427367004,0.0,1.7032834135955746,1.7032834135955746,0,0,0,0.0,0.0;
3,0,0,0.0,9436.39194008105,0.0,0.0,0.0,0.0,2.1487195173520366,411.6574919459044,0.0,1.5821108843618397,1.5821108843618397,0,0,0,0.0,0.0;
9,0,0,0.0,9300.188860728425,0.0,0.0,0.0,0.0,2.0922322396605475,128.50022036906424,0.0,1.5706514400069111,1.5706514400069111,0,0,0,0.0,0.0;
7,0,0,0.0,9250.722735506408,0.0,0.0,0.0,0.0,1.984455642422732,388.9201906318486,0.0,1.5664688568362501,1.5664688568362501,0,0,0,0.0,0.0;
10,0,0,0.0,10921.690389656527,0.0,0.0,0.0,0.0,2.525910059975404,451.73304419890815,0.0,1.702075667961021,1.702075667961021,0,0,0,0.0,0.0;
</species>
<species name="HetSwitchLag3" 
header="family,genealogy,generation,birthday,biomass,inert,capsule,growthRate,volumeRate,locationX,locationY,locationZ,radius,totalRadius,state,turnOn,turnOff,timeRequestTurnOn,timeRequestTurnOff">
11,0,0,0.0,8542.95111576802,0.0,0.0,0.0,0.0,1.7151542880156405,382.0949077168427,0.0,1.5053514092587688,1.5053514092587688,0,0,0,0.0,0.0;
20,0,0,0.0,10745.069584022447,0.0,0.0,0.0,0.0,2.5419699215432465,263.19458526685645,0.0,1.688256960666269,1.688256960666269,0,0,0,0.0,0.0;
16,0,0,0.0,8850.065102530372,0.0,0.0,0.0,0.0,1.6791496600919564,148.3539079205623,0.0,1.5321707444020325,1.5321707444020325,0,0,0,0.0,0.0;
17,0,0,0.0,11334.941609955593,0.0,0.0,0.0,0.0,1.6439537761208118,22.10236786285367,0.0,1.7339779738737258,1.7339779738737258,0,0,0,0.0,0.0;
14,0,0,0.0,8638.242565487682,0.0,0.0,0.0,0.0,1.9155027193295597,421.46814569227325,0.0,1.5137237688378644,1.5137237688378644,0,0,0,0.0,0.0;
12,0,0,0.0,11466.385267459418,0.0,0.0,0.0,0.0,1.5206350101094852,45.20188721061089,0.0,1.7440028799850171,1.7440028799850171,0,0,0,0.0,0.0;
13,0,0,0.0,11093.497658792934,0.0,0.0,0.0,0.0,1.7162395012420204,348.6789232888451,0.0,1.715410961392435,1.715410961392435,0,0,0,0.0,0.0;
18,0,0,0.0,10645.961795157442,0.0,0.0,0.0,0.0,2.3029312588965487,404.03646406841125,0.0,1.6804530547500658,1.6804530547500658,0,0,0,0.0,0.0;
19,0,0,0.0,8418.014077825665,0.0,0.0,0.0,0.0,1.7570640905126498,144.8743349837143,0.0,1.4943033039674238,1.4943033039674238,0,0,0,0.0,0.0;
15,0,0,0.0,10206.581064888482,0.0,0.0,0.0,0.0,1.9239362491213576,228.09896629734396,0.0,1.6454097918832367,1.6454097918832367,0,0,0,0.0,0.0;
</species>
<species name="HetSwitchLag5" 
header="family,genealogy,generation,birthday,biomass,inert,capsule,growthRate,volumeRate,locationX,locationY,locationZ,radius,totalRadius,state,turnOn,turnOff,timeRequestTurnOn,timeRequestTurnOff">
24,0,0,0.0,10576.753299445065,0.0,0.0,0.0,0.0,2.064281466384868,400.1981505067567,0.0,1.6749819069133378,1.6749819069133378,0,0,0,0.0,0.0;
26,0,0,0.0,9440.947889267887,0.0,0.0,0.0,0.0,2.0876309384606353,61.915884790546166,0.0,1.5824927648005653,1.5824927648005653,0,0,0,0.0,0.0;
21,0,0,0.0,9831.60004105263,0.0,0.0,0.0,0.0,2.129612579726256,252.32262463906574,0.0,1.614901486151026,1.614901486151026,0,0,0,0.0,0.0;
25,0,0,0.0,8893.401864401956,0.0,0.0,0.0,0.0,2.1599040719034734,41.48454563271824,0.0,1.5359175095805058,1.5359175095805058,0,0,0,0.0,0.0;
28,0,0,0.0,9796.150540148134,0.0,0.0,0.0,0.0,2.3788989113752264,378.5719493441234,0.0,1.6119874564637684,1.6119874564637684,0,0,0,0.0,0.0;
22,0,0,0.0,10646.768269597578,0.0,0.0,0.0,0.0,2.1026877459254334,407.88326136553883,0.0,1.6805167040847753,1.6805167040847753,0,0,0,0.0,0.0;
23,0,0,0.0,11113.496902032395,0.0,0.0,0.0,0.0,2.123339391441917,0.08626959889139307,0.0,1.7169565277236334,1.7169565277236334,0,0,0,0.0,0.0;
27,0,0,0.0,9535.366822402179,0.0,0.0,0.0,0.0,2.412538578256463,440.2689581500834,0.0,1.5903863341849398,1.5903863341849398,0,0,0,0.0,0.0;
29,0,0,0.0,9194.50077526157,0.0,0.0,0.0,0.0,2.0590925690243482,320.5204694473033,0.0,1.5617014363100443,1.5617014363100443,0,0,0,0.0,0.0;
30,0,0,0.0,10189.834793898333,0.0,0.0,0.0,0.0,1.7209666769662284,425.0943819642817,0.0,1.6440593989478232,1.6440593989478232,0,0,0,0.0,0.0;
</species>

</simulation>
</idynomics>