diff --git a/Proposal/cyto_proposal_draft.rtf b/Proposal/cyto_proposal_draft.rtf index 64f8674..a371058 100644 --- a/Proposal/cyto_proposal_draft.rtf +++ b/Proposal/cyto_proposal_draft.rtf @@ -116,8 +116,8 @@ \leveltemplateid67698715\'02\'05.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fi-180\li4320\lin4320 }{\listlevel\levelnfc0\levelnfcn0\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext \leveltemplateid67698703\'02\'06.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fi-360\li5040\lin5040 }{\listlevel\levelnfc4\levelnfcn4\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext \leveltemplateid67698713\'02\'07.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fi-360\li5760\lin5760 }{\listlevel\levelnfc2\levelnfcn2\leveljc2\leveljcn2\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext -\leveltemplateid67698715\'02\'08.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fi-180\li6480\lin6480 }{\listname ;}\listid1388718708}{\list\listtemplateid1668440594\listhybrid{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0 -\levelstartat1\levelspace0\levelindent0{\leveltext\leveltemplateid67698701\'01\u-3844 ?;}{\levelnumbers;}\f10\fbias0 \fi-360\li720\lin720 }{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0 +\leveltemplateid67698715\'02\'08.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fi-180\li6480\lin6480 }{\listname ;}\listid1388718708}{\list\listtemplateid-1479218694\listhybrid{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0 +\levelstartat1\levelspace0\levelindent0{\leveltext\leveltemplateid67698689\'01\u-3913 ?;}{\levelnumbers;}\f3\fbias0 \fi-360\li720\lin720 }{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0 \levelindent0{\leveltext\leveltemplateid67698691\'01o;}{\levelnumbers;}\f2\fbias0 \fi-360\li1440\lin1440 }{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext \leveltemplateid67698693\'01\u-3929 ?;}{\levelnumbers;}\f10\fbias0 \fi-360\li2160\lin2160 }{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext\leveltemplateid67698689 \'01\u-3913 ?;}{\levelnumbers;}\f3\fbias0 \fi-360\li2880\lin2880 }{\listlevel\levelnfc23\levelnfcn23\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace0\levelindent0{\leveltext\leveltemplateid67698691\'01o;}{\levelnumbers;}\f2\fbias0 @@ -170,11 +170,12 @@ \listoverridecount0\ls2}{\listoverride\listid894318492\listoverridecount0\ls3}{\listoverride\listid197090385\listoverridecount0\ls4}{\listoverride\listid1679115689\listoverridecount0\ls5}{\listoverride\listid1113789639\listoverridecount0\ls6} {\listoverride\listid2003852343\listoverridecount0\ls7}{\listoverride\listid448017185\listoverridecount0\ls8}{\listoverride\listid1836218059\listoverridecount0\ls9}{\listoverride\listid1875802485\listoverridecount0\ls10}{\listoverride\listid380521030 \listoverridecount0\ls11}{\listoverride\listid990597721\listoverridecount0\ls12}{\listoverride\listid1902596172\listoverridecount0\ls13}{\listoverride\listid1624657255\listoverridecount0\ls14}}{\*\pgptbl {\pgp\ipgp0\itap0\li0\ri0\sb0\sa0}{\pgp\ipgp0\itap0 -\li0\ri0\sb0\sa0}}{\*\rsidtbl \rsid661358\rsid811805\rsid987447\rsid1005061\rsid1144518\rsid1978716\rsid2179242\rsid2258122\rsid2885361\rsid3037624\rsid3544762\rsid3686692\rsid3691284\rsid3893994\rsid4095005\rsid4289460\rsid4867986\rsid5642328\rsid6441956 -\rsid7159861\rsid7301558\rsid7351155\rsid7428687\rsid7481430\rsid7871216\rsid7930240\rsid8603549\rsid9125445\rsid9515647\rsid9729187\rsid10749064\rsid10833659\rsid11033285\rsid11420274\rsid11763673\rsid12472430\rsid12605065\rsid12612662\rsid12784431 -\rsid13245809\rsid13452395\rsid13701314\rsid14096627\rsid14227779\rsid14289678\rsid14314780\rsid15139483\rsid15143196\rsid15670606\rsid16068262\rsid16079343\rsid16199571\rsid16257186}{\mmathPr\mmathFont34\mbrkBin0\mbrkBinSub0\msmallFrac0\mdispDef1 -\mlMargin0\mrMargin0\mdefJc1\mwrapIndent1440\mintLim0\mnaryLim1}{\info{\author Abhas Bhattacharya}{\operator Abhas Bhattacharya}{\creatim\yr2013\mo4\dy22\hr21\min35}{\revtim\yr2013\mo4\dy22\hr21\min35}{\version2}{\edmins0}{\nofpages5}{\nofwords1090} -{\nofchars6218}{\nofcharsws7294}{\vern49247}}{\*\xmlnstbl {\xmlns1 http://schemas.microsoft.com/office/word/2003/wordml}}\paperw12240\paperh15840\margl1440\margr1440\margt1440\margb1440\gutter0\ltrsect +\li0\ri0\sb0\sa0}}{\*\rsidtbl \rsid661358\rsid811805\rsid987447\rsid1005061\rsid1144518\rsid1978716\rsid2179242\rsid2258122\rsid2885361\rsid3037624\rsid3544762\rsid3686692\rsid3691284\rsid3888379\rsid3893994\rsid4289460\rsid4867986\rsid5443076\rsid5527469 +\rsid5642328\rsid6441956\rsid6694795\rsid7159861\rsid7301558\rsid7351155\rsid7428687\rsid7481430\rsid7871216\rsid7930240\rsid8021824\rsid8224398\rsid8603549\rsid9125445\rsid9515647\rsid9729187\rsid9976910\rsid10290250\rsid10749064\rsid10833659 +\rsid11033285\rsid11365149\rsid11420274\rsid11763673\rsid12472430\rsid12605065\rsid12612662\rsid12784431\rsid13245809\rsid13452395\rsid13701314\rsid14096627\rsid14227779\rsid14289678\rsid14314780\rsid14497109\rsid14563977\rsid15139483\rsid15143196 +\rsid15670606\rsid16068262\rsid16199571\rsid16257186}{\mmathPr\mmathFont34\mbrkBin0\mbrkBinSub0\msmallFrac0\mdispDef1\mlMargin0\mrMargin0\mdefJc1\mwrapIndent1440\mintLim0\mnaryLim1}{\info{\author Abhas Bhattacharya}{\operator Abhas Bhattacharya} +{\creatim\yr2013\mo4\dy23\hr13\min43}{\revtim\yr2013\mo4\dy23\hr13\min43}{\version2}{\edmins0}{\nofpages5}{\nofwords1090}{\nofchars6217}{\nofcharsws7293}{\vern49247}}{\*\xmlnstbl {\xmlns1 http://schemas.microsoft.com/office/word/2003/wordml}} +\paperw12240\paperh15840\margl1440\margr1440\margt1440\margb1440\gutter0\ltrsect \widowctrl\ftnbj\aenddoc\trackmoves0\trackformatting1\donotembedsysfont1\relyonvml0\donotembedlingdata0\grfdocevents0\validatexml1\showplaceholdtext0\ignoremixedcontent0\saveinvalidxml0\showxmlerrors1\noxlattoyen \expshrtn\noultrlspc\dntblnsbdb\nospaceforul\formshade\horzdoc\dgmargin\dghspace180\dgvspace180\dghorigin1440\dgvorigin1440\dghshow1\dgvshow1 \jexpand\viewkind1\viewscale100\pgbrdrhead\pgbrdrfoot\splytwnine\ftnlytwnine\htmautsp\nolnhtadjtbl\useltbaln\alntblind\lytcalctblwd\lyttblrtgr\lnbrkrule\nobrkwrptbl\snaptogridincell\allowfieldendsel\wrppunct @@ -221,7 +222,7 @@ neration of json representation. Cytoscape-web, the predecessor of Cytoscape.js \par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1005061 Xgmml, Graphml, Sif, Nnf, Gml (,Csv, Xls}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 x}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1005061 ). \par They are arranged according to their priority and so this is the order in which their }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 json }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1005061 converters will be implemented. The last two (in bracket) will be kept as extras, meaning that they will be implemented only if the project is finished well before the deadline (see the timeline for details) . -\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid16079343\charrsid2755305 {\*\shppict{\pict{\*\picprop\shplid1026{\sp{\sn shapeType}{\sv 75}}{\sp{\sn fFlipH}{\sv 0}} +\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid8021824\charrsid10506147 {\*\shppict{\pict{\*\picprop\shplid1026{\sp{\sn shapeType}{\sv 75}}{\sp{\sn fFlipH}{\sv 0}} {\sp{\sn fFlipV}{\sv 0}}{\sp{\sn fLockAspectRatio}{\sv 1}}{\sp{\sn fLockPosition}{\sv 0}}{\sp{\sn fLockAgainstSelect}{\sv 0}}{\sp{\sn fLockAgainstGrouping}{\sv 0}}{\sp{\sn pictureGray}{\sv 0}}{\sp{\sn pictureBiLevel}{\sv 0}}{\sp{\sn fFilled}{\sv 0}} {\sp{\sn fLine}{\sv 0}}{\sp{\sn wzName}{\sv Picture 2}}{\sp{\sn wzDescription}{\sv Description: C:\'5cUsers\'5cAbhas_2\'5cDesktop\'5ccyto\'5ccyto_proposal.png}}{\sp{\sn dhgt}{\sv 251658240}}{\sp{\sn fHidden}{\sv 0}}{\sp{\sn fLayoutInCell}{\sv 1}}} \picscalex90\picscaley90\piccropl0\piccropr0\piccropt0\piccropb0\picw18254\pich12169\picwgoal10349\pichgoal6899\pngblip\bliptag1829957175{\*\blipuid 6d12ee374391210fb1ec76ff23e71ad1} @@ -5625,7 +5626,7 @@ ab02a2a30101010101010101010101010101010101010101019e9fa0220101010101010101010101 \ltrch\fcs0 \insrsid1005061 Xgmml: This is the top priority format and hence will be dealt with first. Xml parsers available in native javascript and jquery will be used for parsing }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid3686692 the xgmml file. Then some JavaScript code}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7301558 (using looping and if needed, regular expressions)}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid3686692 will deal with the pars}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7301558 ed xml file to convert them correctly into javascript variables and objects. Finally, they can be used to generate its json representation.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16257186 - (Maybe, take some inspiration from this library in Gremlin (written in java): }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16079343 HYPERLINK "https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library" } + (Maybe, take some inspiration from this library in Gremlin (written in java): }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8021824 HYPERLINK "https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library" } }{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs20\ul\cf18\insrsid16257186\charrsid15730396 https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj { \rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16257186 )}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7301558 \par }\pard\plain \ltrpar\ql \li720\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid7301558 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 @@ -5642,13 +5643,11 @@ the xgmml file. Then some JavaScript code}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \ins \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid12784431\contextualspace \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 Graphml: Graphml is also a xml-based format, so the implementation process is same as that of the previous one. Only the code will be different to take care of the syntax difference of these formats. \par }\pard \ltrpar\s17\ql \li720\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid12784431\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 -\par Before I move on to the other ones, here is a small chart for reference: -\par -\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12784431 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 -{\rtlch\fcs1 \af31507 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid16079343\charrsid2755305 {\*\shppict{\pict{\*\picprop\shplid1025{\sp{\sn shapeType}{\sv 75}}{\sp{\sn fFlipH}{\sv 0}} +\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8224398 Before I}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 move on to the other ones, here is a small chart for reference: +\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid8021824\charrsid10506147 {\*\shppict{\pict{\*\picprop\shplid1025{\sp{\sn shapeType}{\sv 75}}{\sp{\sn fFlipH}{\sv 0}} {\sp{\sn fFlipV}{\sv 0}}{\sp{\sn fLockAspectRatio}{\sv 1}}{\sp{\sn fLockPosition}{\sv 0}}{\sp{\sn fLockAgainstSelect}{\sv 0}}{\sp{\sn fLockAgainstGrouping}{\sv 0}}{\sp{\sn pictureGray}{\sv 0}}{\sp{\sn pictureBiLevel}{\sv 0}}{\sp{\sn fFilled}{\sv 0}} -{\sp{\sn fLine}{\sv 0}}{\sp{\sn wzName}{\sv Picture 1}}{\sp{\sn wzDescription}{\sv Description: C:\'5cUsers\'5cAbhas_2\'5cDesktop\'5ccyto\'5ccyto_implementation.png}}{\sp{\sn dhgt}{\sv 251658240}}{\sp{\sn fHidden}{\sv 0}}{\sp{\sn fLayoutInCell}{\sv 1}}} -\picscalex78\picscaley78\piccropl0\piccropr0\piccropt0\piccropb0\picw20879\pich12173\picwgoal11837\pichgoal6901\pngblip\bliptag246545358{\*\blipuid 0eb1fbce3fed2e3aecaa23ab16ab124d} +{\sp{\sn fLine}{\sv 0}}{\sp{\sn wzName}{\sv Picture 3}}{\sp{\sn wzDescription}{\sv Description: C:\'5cUsers\'5cAbhas_2\'5cDesktop\'5ccyto\'5ccyto_implementation.png}}{\sp{\sn dhgt}{\sv 251658240}}{\sp{\sn fHidden}{\sv 0}}{\sp{\sn fLayoutInCell}{\sv 1}}} +\picscalex100\picscaley100\piccropl0\piccropr0\piccropt0\piccropb0\picw20879\pich12173\picwgoal11837\pichgoal6901\pngblip\bliptag246545358{\*\blipuid 0eb1fbce3fed2e3aecaa23ab16ab124d} 89504e470d0a1a0a0000000d4948445200000315000001cc08020000002cd11293000000017352474200aece1ce90000000467414d410000b18f0bfc61050000 00097048597300000ec300000ec301c76fa86400004c7f49444154785eeddd7b9015f59df7f19fcf5fe062102a3acb0883cea831c8a54a8a68212ab0868ac44b ad1a940734a6b68895958a3e5e12b36437b7c5356b748d0fbb96a1b6340a0f4ad09497681e34030a52b814a9e22271d5199c611c1cc9c34844e13f9edfadafa7 @@ -5956,7 +5955,7 @@ eb67f6784b327e696f233c9ed054453e0229b27032cc5774e1b7050fb5f0d88acf8889cef641d18f 1273bdf5eaf0f25372f4441dd17e0700406d1ccad0731ccd89fc0400404d0c7567e9398ea6447e0200a07a0ea92b779b5edbbb86e2bf91829641ff270000aac7 ef525de5fece91cedd5272b771d40bf9090000c00ded770000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec8 4f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000006ec84f0000002e84f8ffcaaa6a910996b2e10000000049454e44ae426082}}{\nonshppict -{\pict\picscalex79\picscaley79\piccropl0\piccropr0\piccropt0\piccropb0\picw20879\pich12173\picwgoal11837\pichgoal6901\wmetafile8\bliptag246545358\blipupi95{\*\blipuid 0eb1fbce3fed2e3aecaa23ab16ab124d} +{\pict\picscalex100\picscaley100\piccropl0\piccropr0\piccropt0\piccropb0\picw20879\pich12173\picwgoal11837\pichgoal6901\wmetafile8\bliptag246545358\blipupi95{\*\blipuid 0eb1fbce3fed2e3aecaa23ab16ab124d} 010009000003dac902000000b1c9020000000400000003010800050000000b0200000000050000000c02cd011603030000001e00040000000701040004000000 07010400b1c90200410b2000cc00cc01150300000000cc011503000000002800000015030000cc01000001000800000000000000000000000000000000000000 00000000000000000000ffffff00d3e3ff00a449b300b449a300ffe3d200f0ffff00a46bd200a449a300e1ffff00a449c200c8ffff004cb175006eb12200fff2 @@ -11668,32 +11667,35 @@ b3af0101010101010101010101010101010101010101010101010101010101010101010101010101 01010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101 010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101000000040000002701ffff030000000000}}}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 +\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12784431 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 +{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12784431 \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs22\insrsid10749064 \hich\af31506\dbch\af31506\loch\f31506 3.\tab}}\pard\plain \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid10749064\contextualspace \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10749064 Sif and Nnf: Very simple jS code needs to be written to take care of these file formats. There is already a python-based implementation of these converters (written by me) available at }{\field\fldedit{\*\fldinst {\rtlch\fcs1 -\af31507 \ltrch\fcs0 \insrsid16079343 HYPERLINK "https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py%20%20" }}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs20\ul\cf18\insrsid10749064\charrsid4289460 https://github.com/bendther -ules/GSOC_13/tree/master/nnf_and_sif_to_json_py }}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10749064 . Nnf files will be stripped off its network information an}{\rtlch\fcs1 \af31507 -\ltrch\fcs0 \insrsid4289460 d treated just like a Sif file (Possible problem with multi-network files ??}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10749064 ) +\af31507 \ltrch\fcs0 \insrsid8021824 HYPERLINK "https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py%20%20" }}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs20\ul\cf18\insrsid10749064\charrsid4289460 +https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py }}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10749064 + . Nnf files will be stripped off its network information an}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4289460 d treated just like a Sif file (Possible problem with multi-network files ??}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10749064 ) \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs22\insrsid4289460 \hich\af31506\dbch\af31506\loch\f31506 4.\tab}}\pard \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 -\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid4289460\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4289460 GML: A custom-made parser needs to be built based on regular expressi -ons (native js or possibly using xregexp library }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16079343 HYPERLINK "http://xregexp.com/" }}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs20\ul\cf18\insrsid4289460\charrsid15730396 -http://xregexp.com/}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4289460 ). The rest of the plan is the same as that of xgmml, only this new parser will be used. +\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid4289460\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4289460 GML: A custom-made pa +rser needs to be built based on regular expressions (native js or possibly using xregexp library }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8021824 HYPERLINK "http://xregexp.com/" }}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 +\cs20\ul\cf18\insrsid4289460\charrsid15730396 http://xregexp.com/}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4289460 + ). The rest of the plan is the same as that of xgmml, only this new parser will be used. \par }\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11033285 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 Few words on the extras: -\par These extras will be done only if the -re is ample time left after the completion of the whole project, so there is no way that they will harm the main project. I am aware that new GSOC applicants like me tend to propose a lot more than they can actually complete, so I have tried not to fall i -n that trap. But these extras are here, because I plan to do them in the future, within or after GSOC. Also, as a side note, in future, I wish to release this codes as a separate jS library for }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14289678 -converting customized}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 -xml formats into json (I hope my mentoring org will allow this). +\par These extras will be done only if there is ample time left after the completion of the whole project, so there is no way that they will harm the main project. I am aware that new GSOC applicants like me tend to propose a lot more than they can a +ctually complete, so I have tried not to fall in that trap. But these extras are here, because I plan to do them in the future, within or after GSOC. Also, as a side note, in future, I wish to release this codes as a separate jS library for }{ +\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14289678 converting customized}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 -xml formats into json (I hope my mentoring org will allow this). \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs22\insrsid11033285 \hich\af31506\dbch\af31506\loch\f31506 5.\tab}}\pard\plain \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid3893994\contextualspace \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 Csv: Use any well-documented csv parser and rest is the same.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid3893994 \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs22\insrsid11033285 \hich\af31506\dbch\af31506\loch\f31506 6.\tab}}\pard \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin720\itap0\pararsid15139483\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 Xlsx: This is the most challenging part. I wouldn\rquote -t have tried this if there was no cross-}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12472430 browser external}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 library to read and write xlsx format. But thankfully and qui -te surprisingly, there is one called Xlsx.js }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16079343 HYPERLINK "https://github.com/stephen-hardy/xlsx.js" }}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 -\cs20\ul\cf18\insrsid11033285\charrsid15730396 https://github.com/stephen-hardy/xlsx.js}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 .}{\rtlch\fcs1 \af31507 \ltrch\fcs0 -\insrsid10833659 I am }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 not much sure if I can pull off this part}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7351155 , but I am still including this in the proposal mostly for my ins -piration than anything else.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid15139483 Also, I know that the Cytoscape project originally supported .xls, but I think its best kept to Microsoft Excel for converting .xls into .xlsx . +t have tried this if there was no cross-}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12472430 browser external}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 library to re +ad and write xlsx format. But thankfully and quite surprisingly, there is one called Xlsx.js }{\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8021824 HYPERLINK "https://github.com/stephen-hardy/xlsx.js" }}{\fldrslt {\rtlch\fcs1 +\af31507 \ltrch\fcs0 \cs20\ul\cf18\insrsid11033285\charrsid15730396 https://github.com/stephen-hardy/xlsx.js}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 .}{\rtlch\fcs1 +\af31507 \ltrch\fcs0 \insrsid10833659 I am }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11033285 not much sure if I can pull off this part}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7351155 , but I am still +including this in the proposal mostly for my inspiration than anything else.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid15139483 + Also, I know that the Cytoscape project originally supported .xls, but I think its best kept to Microsoft Excel for converting .xls into .xlsx . \par }\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid661358 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 { \rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid661358 \par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\sl276\slmult1\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid14289678 \rtlch\fcs1 \ab\af31503\afs28\alang1025 \ltrch\fcs0 @@ -11762,20 +11764,19 @@ July 30: Take a day off from coding and analyze what went right and wrong in the \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs20\insrsid7871216 \hich\af31506\dbch\af31506\loch\f31506 2.\tab}}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7871216 Make sure the regular-expression based Gml parser is not buggy. \par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f31506\fs20\insrsid7871216 \hich\af31506\dbch\af31506\loch\f31506 3.\tab}The input graph formats might not be well-formed (if manually created). (Maybe, add a }{\rtlch\fcs1 -\af31507 \ltrch\fcs0 \insrsid1978716 xml-}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7871216 checker and discard non well-formed files.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14314780 Such a checker might not be possible in case of -non-xml based formats}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14096627 .}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7871216 ) +\af31507 \ltrch\fcs0 \insrsid1978716 xml-}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7871216 checker and discard non well-formed files.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14314780 S +uch a checker might not be possible in case of non-xml based formats}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14096627 .}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7871216 ) \par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\sl276\slmult1\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid9515647 \rtlch\fcs1 \ab\af31503\afs28\alang1025 \ltrch\fcs0 \b\fs28\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \insrsid9515647 \hich\af31502\dbch\af31501\loch\f31502 What can I bring to the team? \par }\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9515647 \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 { \rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9515647\charrsid9515647 -\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f10\fs22\insrsid9515647 \loch\af10\dbch\af31506\hich\f10 \'fc\tab}}\pard\plain \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 +\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f3\fs22\insrsid9515647 \loch\af3\dbch\af31506\hich\f3 \'b7\tab}}\pard\plain \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls14\adjustright\rin0\lin720\itap0\pararsid9515647\contextualspace \rtlch\fcs1 \af31507\afs22\alang1025 \ltrch\fcs0 \f31506\fs22\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 -\ltrch\fcs0 \insrsid9515647 Yes, I am committed in working hard for this GSOC project this summer. }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1144518 - I do not have any other commitment during the summer other than my college internals for the next session which should be held n -ear the end of August or the start of September. I am not yet sure about the date, but I will ask for a one-week break during that time. I hope it won\rquote t be much of a problem. -\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f10\fs22\insrsid9515647 \loch\af10\dbch\af31506\hich\f10 \'fc\tab}}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9515647 -Being my first GSOC project, I am also super-excited about it, can\rquote t wait to have a fruitful summer this year. -\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f10\fs22\insrsid12612662 \loch\af10\dbch\af31506\hich\f10 \'fc\tab}}\pard \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 +\ltrch\fcs0 \insrsid9515647 Yes, I am committed in working hard for this GSOC project this summer. }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1144518 I do not have any other commitment during the summer other than my college intern +als for the next session which should be held near the end of August or the start of September. I am not yet sure about the date, but I will ask for a one-week break during that time. I hope it won\rquote t be much of a problem. +\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f3\fs22\insrsid9515647 \loch\af3\dbch\af31506\hich\f3 \'b7\tab}}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9515647 Being my first GSOC project, I am also super-excited about it, can +\rquote t wait to have a fruitful summer this year. +\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \af31507\afs22 \ltrch\fcs0 \f3\fs22\insrsid12612662 \loch\af3\dbch\af31506\hich\f3 \'b7\tab}}\pard \ltrpar\s17\ql \fi-360\li720\ri0\sa200\sl276\slmult1 \widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls14\adjustright\rin0\lin720\itap0\pararsid987447\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid12612662 I wish to learn some more about the core Cytoscape project but as I am not a Java developer, I wish to linger with the Cytoscape.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid14227779 js project}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7159861 .}{ \rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid987447\charrsid9515647 @@ -11884,8 +11885,8 @@ fffffffffffffffffdfffffffeffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff -ffffffffffffffffffffffffffffffff52006f006f007400200045006e00740072007900000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016000500ffffffffffffffffffffffff0c6ad98892f1d411a65f0040963251e5000000000000000000000000d0fc -ba31733fce01feffffff00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff00000000000000000000000000000000000000000000000000000000 +ffffffffffffffffffffffffffffffff52006f006f007400200045006e00740072007900000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016000500ffffffffffffffffffffffff0c6ad98892f1d411a65f0040963251e50000000000000000000000004057 +9b72fa3fce01feffffff00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff00000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff0000000000000000000000000000000000000000000000000000 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff000000000000000000000000000000000000000000000000 0000000000000000000000000000000000000000000000000105000000000000}} \ No newline at end of file