tag:blogger.com,1999:blog-70538477332457464102024-03-05T01:06:33.956-08:00GSoC 2016 - CellDesignerAnonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-7053847733245746410.post-91211951285013271482016-08-22T23:05:00.001-07:002016-08-22T23:24:50.328-07:00Final ReportHello everyone,<br />
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As the GSoC come to an end, I would like to sum up what I have done for the past 4 months. For my GSoC project, I have been working on the<a href="https://summerofcode.withgoogle.com/dashboard/project/5659317147533312/overview/"> <span style="background-color: white; color: rgba(0 , 0 , 0 , 0.870588); font-family: "roboto" , "helvetica neue" , sans-serif; font-size: 16px; letter-spacing: 0.16px; line-height: 25.6px;">Interconvertible Layout program for CellDesigner</span></a>. This project implements a converter that turns<a href="http://celldesigner.org/documents/CellDesigner4ExtensionTagSpecificationE.pdf"> CellDesigner annotation</a> into <a href="http://sbml.org/Special/specifications/sbml-level-3/version-1/layout/sbml-layout-version-1-release-1.pdf">SBML Layout package</a> and vice versa, preserving the biochemical network layouts when handling the model in different softwares.<br />
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Here is a link to this project's repository.<br />
<a href="https://github.com/funasoul/celldesigner-parser">https://github.com/funasoul/celldesigner-parser</a><br />
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For my last result, I will present the conversion of influenza model (<span style="background-color: white; color: #222222; font-family: "arial" , sans-serif; font-size: 13px; line-height: 16.12px;">Matsuoka,Y. </span><i style="background-color: white; color: #222222; font-family: Arial, sans-serif; font-size: 13px; line-height: 16.12px;">BMC systems biology</i><span style="background-color: white; color: #222222; font-family: "arial" , sans-serif; font-size: 13px; line-height: 16.12px;"> 7.1 (2013): 1.</span>) and Core metabolism model of E.coli <a href="https://www.blogger.com/(http://escher.github.io/">(http://escher.github.io/</a>) converted with <a href="http://escher.readthedocs.io/en/stable/escherconverter.html">EscherConverter</a>.<br />
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CellDesigner to SBML Layout<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDAT7mr9nPj5NB75CaW3AlC0Rl3JvDYn4uJsapkT62mYvOzjcFS_3fU49L7BwFRIsbkgbS6huiHNGA4XFbmG8xhTQnnsta_mIxKInB6IwiOjiPkNQ2779KVfwYPLZYkwbdpEB6rnes6jEo/s1600/influenza.png" imageanchor="1"><img border="0" height="104" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDAT7mr9nPj5NB75CaW3AlC0Rl3JvDYn4uJsapkT62mYvOzjcFS_3fU49L7BwFRIsbkgbS6huiHNGA4XFbmG8xhTQnnsta_mIxKInB6IwiOjiPkNQ2779KVfwYPLZYkwbdpEB6rnes6jEo/s200/influenza.png" width="200" /></a><br />
Influenza model original
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXKaxgZIPaUBeM6iocDpjRxXyhunHSo_K51W5y8wCK0kC_6VWtPsXQJq_gqHflmZhvbJWN-Ops665c4wh-lE0ESjQ94wguIx8jkk2sOSMH7YhY7_s9jDBR-fgHr4PO1Z6_Jt8pMhe7bpZs/s1600/influenza_converted.png" imageanchor="1"><img border="0" height="104" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXKaxgZIPaUBeM6iocDpjRxXyhunHSo_K51W5y8wCK0kC_6VWtPsXQJq_gqHflmZhvbJWN-Ops665c4wh-lE0ESjQ94wguIx8jkk2sOSMH7YhY7_s9jDBR-fgHr4PO1Z6_Jt8pMhe7bpZs/s200/influenza_converted.png" width="200" /></a><br />
Influenza model converted
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SBML Layout to CellDesigner<br />
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<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjqbQgUrJaFfQsCIwvQCwauUN4-lYadJV8nvfyFz27zjOFrNuP-DOzJ7LLqcjTedtniHMpxmtERUt35XedLIga0xV1G5ubbJJKqZQFha8Die9Gfwg-GbpiKZg0Jkxa6aqMPjGLpni2rRED/s1600/ecoli.png" imageanchor="1"><img border="0" height="154" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjqbQgUrJaFfQsCIwvQCwauUN4-lYadJV8nvfyFz27zjOFrNuP-DOzJ7LLqcjTedtniHMpxmtERUt35XedLIga0xV1G5ubbJJKqZQFha8Die9Gfwg-GbpiKZg0Jkxa6aqMPjGLpni2rRED/s200/ecoli.png" width="200" /></a><br />
E.coli model original
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1RX36VtZgmQzp7tFsl5IJF4sTTC7RdqORgI-t5FfGKjfKsNtmlus18pwgG3oJgvfp3Qiu0K07NYEOTDDfpFQs7oXhTiOhAIAxtlYklAvkHIog0_bPXfbbvMX90fJT3WkseGQQbT8XelUh/s1600/ecoli_converted.png" imageanchor="1"><img border="0" height="154" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1RX36VtZgmQzp7tFsl5IJF4sTTC7RdqORgI-t5FfGKjfKsNtmlus18pwgG3oJgvfp3Qiu0K07NYEOTDDfpFQs7oXhTiOhAIAxtlYklAvkHIog0_bPXfbbvMX90fJT3WkseGQQbT8XelUh/s200/ecoli_converted.png" width="200" /></a><br />
E.coli model converted
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Finally, I would like to thank Google Summer of Code, NRNB, and SBML team for giving me this opportunity and my mentors Dr. Dräger and Dr. Funahashi for their support.Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-88702290732013056872016-08-17T07:39:00.003-07:002016-08-20T01:14:19.339-07:00Final week (week 16)Hi all,<br />
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Only few more days are left until I submit my work. And last week, I left off with some unfinished tasks. Here are the todo list from last week. Darker blue means for the conversion from SBML Layout to CellDesigner Annotation and lighter blue means for the conversion from CellDesigner Annotation to SBML Layout.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcjfSc_5kcq_PjpFnz_RhtH28zlX2IhFpZkmhH9cNLL3RZGo3kmwWtxnrQqxAuSSCwxHjpTFtSyDiixPhESMvmxPXkIISCOamtAuhf_lZgvAowqrLdhquvq7Z7CuEN7N_U3ANEuifLIJiB/s1600/Todo+List.png" imageanchor="1"><img border="0" height="284" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcjfSc_5kcq_PjpFnz_RhtH28zlX2IhFpZkmhH9cNLL3RZGo3kmwWtxnrQqxAuSSCwxHjpTFtSyDiixPhESMvmxPXkIISCOamtAuhf_lZgvAowqrLdhquvq7Z7CuEN7N_U3ANEuifLIJiB/s320/Todo+List.png" width="320" /></a><br />
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For this week, I have mainly worked on 1st, 3rd, and 4th tasks. As for the conversion of bezier curve, I have converted the bezier curve into line segments, since CellDesigner does not allow a bezier curve with the reaction with one reactant and one product.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEicJdpOEvqEBl_26l9pSuy2ahZwDCjFHQTiGZYshlA8oZ2MKTdGBTlp5jiPYi6tX6qIDFImaC-UUqwFLlUYT2Y8Cp4zV7RmR7DLCl1dSILal3cm-j2MP5fFRlo91zAjITgM6ngWGi3Rsl/s1600/bezier.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEicJdpOEvqEBl_26l9pSuy2ahZwDCjFHQTiGZYshlA8oZ2MKTdGBTlp5jiPYi6tX6qIDFImaC-UUqwFLlUYT2Y8Cp4zV7RmR7DLCl1dSILal3cm-j2MP5fFRlo91zAjITgM6ngWGi3Rsl/s200/bezier.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRaGZVY2ZDcllWdWs">Bezier original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCQeZOPY5D_Z7kepSylA2V7BATdxuqr4H66SBK5kxaVlGB4hMD43PrgOzyWZyt8jTce5ILeAGpWvRpVLoXA-iNsgIO7AwtvHcLkLqGfZxUFqNZtPmlDMj-yuhTglk6meM2q1n1c_uJTWsb/s1600/bezier_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCQeZOPY5D_Z7kepSylA2V7BATdxuqr4H66SBK5kxaVlGB4hMD43PrgOzyWZyt8jTce5ILeAGpWvRpVLoXA-iNsgIO7AwtvHcLkLqGfZxUFqNZtPmlDMj-yuhTglk6meM2q1n1c_uJTWsb/s200/bezier_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRR1F6MmI3Y1BDb0E">Bezier converted</a></td>
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For the 3rd task, I have added conversion for reaction with modifiers with branches.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_ziyHwNiW-ZWV59CEQ8FCHW6cb7I8JV-tNTyNkVVibB8QK-_GQUimwUBzdLUc3gV5VAqaErKecL7dFg8JFVGUjIQ3YfxFXb8kqA6UMnakOFvbn-W_fLW4QGiYcI8Ep-pJrz5yNTwniUvV/s1600/modifier.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_ziyHwNiW-ZWV59CEQ8FCHW6cb7I8JV-tNTyNkVVibB8QK-_GQUimwUBzdLUc3gV5VAqaErKecL7dFg8JFVGUjIQ3YfxFXb8kqA6UMnakOFvbn-W_fLW4QGiYcI8Ep-pJrz5yNTwniUvV/s200/modifier.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncROTh1YVdHUmRQME0">Modifier with branches original</a>
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJGZWP3ST0psEBeDvAudj7xLk4ZFw_ETebbZSrhEm9JaejVfkAIgDN7IcDDnWKOt6eZeY3cwwVlI0ZTxgLq4p7b4OhV1jzOd6bAD79nt-ew0jLJU4dmM9a1ckAvykOPQi9uvmAQmEKhsV1/s1600/modifier_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJGZWP3ST0psEBeDvAudj7xLk4ZFw_ETebbZSrhEm9JaejVfkAIgDN7IcDDnWKOt6eZeY3cwwVlI0ZTxgLq4p7b4OhV1jzOd6bAD79nt-ew0jLJU4dmM9a1ckAvykOPQi9uvmAQmEKhsV1/s200/modifier_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRQmZpaG9pRFoxM1E">Modifier with branches converted</a>
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Also, for the 4th task, adjusting the arrowhead, I have moved the end point of the line segment to go to the boundary of the glyph.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEpOMIryNT6rBeH45uwj01w0Sz-069qWxHFYLso8YAwiNumW03crvfolkXua1T2Ye9dy9xTdNJJKDScbeg-JlvaUYkwPTkAQLxWurodQXi-klIVFCabVZvf0NQP6NAaS-AoRH33myEeFF8/s1600/arrowhead_before.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEpOMIryNT6rBeH45uwj01w0Sz-069qWxHFYLso8YAwiNumW03crvfolkXua1T2Ye9dy9xTdNJJKDScbeg-JlvaUYkwPTkAQLxWurodQXi-klIVFCabVZvf0NQP6NAaS-AoRH33myEeFF8/s200/arrowhead_before.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVDJmMEw4M1Fsam8">arrowhead before</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg7sXiU5dk-Rz3VowUwXi6dyqy6VDffLtFKD8KL_2y7FLdknacfnRwUA39XptGSZCsAkqiYNpbe5LwMOYLKyHOHbC1tcVdesbM6PijcK-dNZ__BH1LKjE47WPDpf_Cgkcu_FKlTwIkC-yG/s1600/arrowhead_after.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg7sXiU5dk-Rz3VowUwXi6dyqy6VDffLtFKD8KL_2y7FLdknacfnRwUA39XptGSZCsAkqiYNpbe5LwMOYLKyHOHbC1tcVdesbM6PijcK-dNZ__BH1LKjE47WPDpf_Cgkcu_FKlTwIkC-yG/s200/arrowhead_after.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVVJaVEZUS0psQ2s">arrowhead after</a></td>
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Additionally, I have fixed the conversion for FBC package. I have added the conversion for reaction with boolean logic operators.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSoV3r7RTQmfU9q4odLEtTevms53NuWytOSRvWOaKhHETB6G_ZJiKsZJG6VMBReAjfvt3tNI9UwN6rQgReA21Bt8q3LdHtyDf8mTWskFxOtsCG01DWrrdlrpLB5B3iHFGvTr7UozGhtCiD/s1600/boolean.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSoV3r7RTQmfU9q4odLEtTevms53NuWytOSRvWOaKhHETB6G_ZJiKsZJG6VMBReAjfvt3tNI9UwN6rQgReA21Bt8q3LdHtyDf8mTWskFxOtsCG01DWrrdlrpLB5B3iHFGvTr7UozGhtCiD/s200/boolean.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRSWlNejhFZGdqRVU">boolean model</a></td>
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNnV2SFQxa2kyYnM">boolean model converted</a> </td> </tr>
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So for the next few days, I have to work on the 2nd task and wrap up the project.</div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-5065134621081923732016-08-10T04:57:00.000-07:002016-08-20T01:14:06.818-07:00week 15Hello everyone,<br />
<br />
Last week, I left off with the following tasks. So, this week I have been working on these. In particular, I have been working on the 1st, 2nd, 3rd, 5th, and 6th tasks from the top.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGQLI52mIiL0p4YXDIFTvwDWhEWA8UZQD6PKPW1dN2i3Xg6Bd0etSG8gotZNL7MqqFajD4jxUNtnKzBVQdLwS0P5ikhccofkyvIhnJGfB-F9-PMsAVJfy6JqQkpE35ZeHAoM7P3Uq0By1x/s1600/Todo+List.png" imageanchor="1"><img border="0" height="197" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGQLI52mIiL0p4YXDIFTvwDWhEWA8UZQD6PKPW1dN2i3Xg6Bd0etSG8gotZNL7MqqFajD4jxUNtnKzBVQdLwS0P5ikhccofkyvIhnJGfB-F9-PMsAVJfy6JqQkpE35ZeHAoM7P3Uq0By1x/s200/Todo+List.png" width="200" /></a><br />
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For the first three tasks, it is still in progress. I am struggling with the conversion of edit points. But I managed to complete the conversion for some of the reaction.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibLQ-rYf36azyc6Kr9Q92cwQpcGZ2HpjEvBoT6zYWuba_Fw3u2qqo5Da_41Tji7CEdr713Jrazif-65liWEz7qLGqhxLeJ1hFz3bcfq0mxKJpQuAGB2d8pR2RHZtjITtjN-0eSwdOXZwzW/s1600/heterodimer_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibLQ-rYf36azyc6Kr9Q92cwQpcGZ2HpjEvBoT6zYWuba_Fw3u2qqo5Da_41Tji7CEdr713Jrazif-65liWEz7qLGqhxLeJ1hFz3bcfq0mxKJpQuAGB2d8pR2RHZtjITtjN-0eSwdOXZwzW/s200/heterodimer_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRdGRQTGZXQ09pTnM">heterodimer association</a><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5vw-0EZIUDD5zBFarQ3rK7PI6F_lJAvT4onsUWhjWkAwPGQLyhNaJuJ11gF2fhRVD7SuOAiPO4HArcHikbUw7f1gE-jnF6Ja9SNgnuDdZoJJK19coyQU3xJ4IC0KihJc0Y0PDTINN663r/s1600/heterodimer_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5vw-0EZIUDD5zBFarQ3rK7PI6F_lJAvT4onsUWhjWkAwPGQLyhNaJuJ11gF2fhRVD7SuOAiPO4HArcHikbUw7f1gE-jnF6Ja9SNgnuDdZoJJK19coyQU3xJ4IC0KihJc0Y0PDTINN663r/s200/heterodimer_converted_converted.png" width="200" /></a><a href="https://drive.google.com/open?id=0B7QYEhcLQncRLTAxcEZQWEpaT0E"><br /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRLTAxcEZQWEpaT0E">heterodimer association converted</a><br />
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For the 5th task (adjusting text glyph), the text for the reaction is adjusted to go in the center of reaction. The previous implementation laid the text glyph near a reactant, but now I have changed that to go into center of the reaction<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwDEBDPDpGCenATZ_TIgXjNRRebnrQmU-FaWR1_8Corg8731HtqqU5E0GGYGbx_Sd2PeDdZ-WpJRS_2pT82AX0QAMbzAo3B2yWEWCKY0xr7FZyODVOZ8oRnNpOPyLoxxi1daOTsygTKclD/s1600/link.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwDEBDPDpGCenATZ_TIgXjNRRebnrQmU-FaWR1_8Corg8731HtqqU5E0GGYGbx_Sd2PeDdZ-WpJRS_2pT82AX0QAMbzAo3B2yWEWCKY0xr7FZyODVOZ8oRnNpOPyLoxxi1daOTsygTKclD/s200/link.png" width="200" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwDEBDPDpGCenATZ_TIgXjNRRebnrQmU-FaWR1_8Corg8731HtqqU5E0GGYGbx_Sd2PeDdZ-WpJRS_2pT82AX0QAMbzAo3B2yWEWCKY0xr7FZyODVOZ8oRnNpOPyLoxxi1daOTsygTKclD/s1600/link.png" imageanchor="1"></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj891Od-T4tfFu0l7L-oHUSSjYqeaO094bu_HJ5n0czQmF1oFP-db_76pBD-ambVUWzOrNc77ceTzx5ukQDQ2OkpCx9BR6KQsePILrAYJAPXgRD1roh7QqywOjYLYCpbrEyLS0xTDUfXM7i/s1600/layout.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj891Od-T4tfFu0l7L-oHUSSjYqeaO094bu_HJ5n0czQmF1oFP-db_76pBD-ambVUWzOrNc77ceTzx5ukQDQ2OkpCx9BR6KQsePILrAYJAPXgRD1roh7QqywOjYLYCpbrEyLS0xTDUfXM7i/s200/layout.png" width="200" /></a><br />
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before adjustment after adjustment<br />
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For the 6th task, I have added the conversion of gene on CellDesigner Annotation to the SBML fbc package.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqhVri6mwcufnEfkanOl31O1bqkQd6QSYvIPrQf0IZBdTnhgI5mlldg4e-vieOfEKl0FvRE_QmSdFR4fgc_mKzAbMsoHgQhu1FEH2HNaATZLJ7h1UvZJfZqpW-lbAOAJm_OREXYvHJkYYx/s1600/transcription_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqhVri6mwcufnEfkanOl31O1bqkQd6QSYvIPrQf0IZBdTnhgI5mlldg4e-vieOfEKl0FvRE_QmSdFR4fgc_mKzAbMsoHgQhu1FEH2HNaATZLJ7h1UvZJfZqpW-lbAOAJm_OREXYvHJkYYx/s200/transcription_converted_converted.png" width="200" /></a><a href="https://drive.google.com/open?id=0B7QYEhcLQncRaVVnT1J2RWxGejg"><br /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRaVVnT1J2RWxGejg">fbc converted model</a></td>
<td><br />
<br /></td>
</tr>
<tr>
<td><br />
Here is the diagram of how much of the conversion is covered. <span style="background-color: white; color: #333333; font-family: "arial" , "tahoma" , "helvetica" , "freesans" , sans-serif; font-size: 13px; line-height: 18.2px;">Blue means it's completed, red means it's not yet completed, green means it's unconvertable.</span><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHHyyRtY8hK1_49nwg6LPaehv7EeDCh62fm2T9hCpW8ec9KqU0L46Dnah3RedecipOkcH7fnZ2QaysV4f_EnmDwfdqPwjPOdl2y8pMxdO7D0wow6HZRnYvE7ssUZlqsVe3EKUU0QauHdLI/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHHyyRtY8hK1_49nwg6LPaehv7EeDCh62fm2T9hCpW8ec9KqU0L46Dnah3RedecipOkcH7fnZ2QaysV4f_EnmDwfdqPwjPOdl2y8pMxdO7D0wow6HZRnYvE7ssUZlqsVe3EKUU0QauHdLI/s320/CellDesigner+Annotation.png" width="320" /></a><br />
<br /></td><td><br /></td></tr>
<tr><td>Next week is going to be the last week of Google Summer of Code. Below is the tasks that I still need to work on. I am hoping to complete at least the top 5 tasks before the deadline.<br />
<br />
<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTvAQGpOkkwQAJNgaryRUQr1_Fxh8387iMGkzDHOmA3Os-cNB3BTHPmcyi5kxI6cAsSgsKDpAgiEZ_MepCa-aeFirfcg6lC9nBU3QS-LJR7g8ywEdlF6NSfVfqLhG8ot5nu9zUJ8X9rsae/s1600/Todo+List.png" imageanchor="1"><img border="0" height="284" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTvAQGpOkkwQAJNgaryRUQr1_Fxh8387iMGkzDHOmA3Os-cNB3BTHPmcyi5kxI6cAsSgsKDpAgiEZ_MepCa-aeFirfcg6lC9nBU3QS-LJR7g8ywEdlF6NSfVfqLhG8ot5nu9zUJ8X9rsae/s320/Todo+List.png" width="320" /></a></td><td><br /></td></tr>
</tbody></table>
</div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com1tag:blogger.com,1999:blog-7053847733245746410.post-40454090710914567212016-08-03T05:02:00.001-07:002016-08-20T01:13:58.358-07:00Week 14Hello everyone,<br />
<br />
This week, I have been working on reactions with branches. I was able to convert the branched reactions only with the one that have single reactant and product. For the reaction with multiple reactants/products, the conversion for connecting point is a bit off. I assume there is something wrong in the algorithm.<br />
<br />
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<div class="table-responsive">
<table class="table table-bordered table-striped">
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgD2i9SlRWErTFK6bdKPE0Z__ETijfmT15BRENc9cBMvLJTaWa2ZrUGejFhWRMa6-4vb6dGaezKY4wMfriDiyZEry-oubUPPNUTiRg7bgKBBiSFyimodlo5x01VpqNGh-oA23E7qEz4qy7q/s1600/basic2_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgD2i9SlRWErTFK6bdKPE0Z__ETijfmT15BRENc9cBMvLJTaWa2ZrUGejFhWRMa6-4vb6dGaezKY4wMfriDiyZEry-oubUPPNUTiRg7bgKBBiSFyimodlo5x01VpqNGh-oA23E7qEz4qy7q/s200/basic2_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWUoyV2FqVmdzc2c">bend model original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-C-QZhxqeHhtr_9EAwz4pdj7rpvQwPWC040969KhlxbJgTtXFWbGbv1GBH5uK-P5tiwZZv_oaKO_D3grRnPyOiGfSrEI6jbGaUDWqRqzFjRCw8ASSE8MRlPcYGYY8jpYub7GERJGcGwEN/s1600/basic2_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-C-QZhxqeHhtr_9EAwz4pdj7rpvQwPWC040969KhlxbJgTtXFWbGbv1GBH5uK-P5tiwZZv_oaKO_D3grRnPyOiGfSrEI6jbGaUDWqRqzFjRCw8ASSE8MRlPcYGYY8jpYub7GERJGcGwEN/s200/basic2_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWjJ1V1RwZllYZW8">bend model converted</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZeXRuwX0wCjK7xkDROUPfoLmogv0VZyNlR9aceviu-XzypMY7wZ1DzWEVrdQcz6BnTTrjpy7wcJelC7Aeo6Cjq2AucdvdOjh8OBNgWDacUlDV6k-1qDev6Oz8ONe9vteQLu-JfrMx486y/s1600/basic3_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZeXRuwX0wCjK7xkDROUPfoLmogv0VZyNlR9aceviu-XzypMY7wZ1DzWEVrdQcz6BnTTrjpy7wcJelC7Aeo6Cjq2AucdvdOjh8OBNgWDacUlDV6k-1qDev6Oz8ONe9vteQLu-JfrMx486y/s200/basic3_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRSjBXRUJMVWZFX00">bend model 2 original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_3dNz0N3rCNXuclbCuMNkpdWOARrtP2KEXnM6YRKP8FefbhjVmNO7bzMxDLvyyprEsWR-Hpkfo-n-1TZZ1h6wFr2oLGgea-dgtpy3riZ7uBpq7LfXW6ERNn9vFHzrfG31bM_kgATXZGGv/s1600/basic3_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_3dNz0N3rCNXuclbCuMNkpdWOARrtP2KEXnM6YRKP8FefbhjVmNO7bzMxDLvyyprEsWR-Hpkfo-n-1TZZ1h6wFr2oLGgea-dgtpy3riZ7uBpq7LfXW6ERNn9vFHzrfG31bM_kgATXZGGv/s200/basic3_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVDFlelU4bzc5a2c">bend model 2 converted</a></td>
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhumAnMYAeoJU_sqRGgtu6xaTkGa2QSx5qAPebS0CBWtR_-NARxsg6iOINl5D9M6fUcizz-PRYEF5ND6ZEhZQkIjcLbH_aU2t9YM7tnOG2x4gWG_6SO78kRtfHW1kdAL84crp01DQ_GVHsR/s1600/heterodimer.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhumAnMYAeoJU_sqRGgtu6xaTkGa2QSx5qAPebS0CBWtR_-NARxsg6iOINl5D9M6fUcizz-PRYEF5ND6ZEhZQkIjcLbH_aU2t9YM7tnOG2x4gWG_6SO78kRtfHW1kdAL84crp01DQ_GVHsR/s200/heterodimer.png" width="200" /></a><br />
bend model 3 original
</td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6mzR8tePs0C_o-C0R7VodE6boA31PVlwhAbdVz3KgqJpnoDFmiI__JQELZj-KOmgL-4gZ1HYGvB2LXNuHwvCUE1p7eowDMcGUUovL0l2IYGueOHzGAQZIKbT-4JEV-QBuDz4QLMVZFQMl/s1600/heterodimer_converted2_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6mzR8tePs0C_o-C0R7VodE6boA31PVlwhAbdVz3KgqJpnoDFmiI__JQELZj-KOmgL-4gZ1HYGvB2LXNuHwvCUE1p7eowDMcGUUovL0l2IYGueOHzGAQZIKbT-4JEV-QBuDz4QLMVZFQMl/s200/heterodimer_converted2_converted.png" width="200" /></a><br />
bend model 3 converted
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</tbody>
</table>
</div>
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So far, for the conversion from SBML Layout to CellDesigner annotation, I have completed the following shown in the chart below. Blue is completed, red is incomplete, and green is inconvertable.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisxsanAZlRCkZyswSb2dArcXCJgonQR0sq_oHFeEqibhMOjZ9awS0tIj8YrDvFIS8Fahyphenhyphen6StR7l69KUSMgpR_ADE9_9SSuY4kM5xO7OBtNxXkwa8wJwla8fukUUK6yQ9k_QAeKVngwImvG/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisxsanAZlRCkZyswSb2dArcXCJgonQR0sq_oHFeEqibhMOjZ9awS0tIj8YrDvFIS8Fahyphenhyphen6StR7l69KUSMgpR_ADE9_9SSuY4kM5xO7OBtNxXkwa8wJwla8fukUUK6yQ9k_QAeKVngwImvG/s320/CellDesigner+Annotation.png" width="320" /></a></div>
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Also, the remaining tasks for this project is as below. The dark blue is for conversion from SBML Layout to CellDesigner annotation, and the light blue if for conversion from CellDesigner annotation to SBML Layout. For next week, I will be working on the tasks on the top. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZqBktgEVVoKrs_DaAWmCAvzbMKxvQsZvEaTmzM2NbexEuLujaeJnhRsGZnBcI-Qnc_XR7E2YVjxidQwJv0L5Pcb1TqkJGWl6qi2q3vCWkH7zaizxIyr6mMiRzhpeJ8h-GFYPwCVIUDXqH/s1600/Todo+List.png" imageanchor="1"><img border="0" height="197" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZqBktgEVVoKrs_DaAWmCAvzbMKxvQsZvEaTmzM2NbexEuLujaeJnhRsGZnBcI-Qnc_XR7E2YVjxidQwJv0L5Pcb1TqkJGWl6qi2q3vCWkH7zaizxIyr6mMiRzhpeJ8h-GFYPwCVIUDXqH/s200/Todo+List.png" width="200" /></a></div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-25942129544961856802016-07-27T09:21:00.001-07:002016-08-20T01:13:46.998-07:00Week 13Hello everyone,<br />
<br />
<br />
This week I have been working on the reaction conversion from SBML Layout to CellDesigner annotation. Last week, I have completed converting reactions with 1 reactant and 1 product with 1 modifier. For this week, I have completed converting reactions with multiple reactants/ products and with bezier curve.<br />
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3e_TXrv6vl533e6dNw56vk5FaPfbIOAC1lKoPpdZwVGEHNHlny77k7w2qyanZnToLnpWuk88nXf11Oix-M73YrJAcsdCByETvHFuOyvD3DgNRMlGSo6OUHMTicumd0dQth4JaAGDHRpFD/s1600/s_converted.png" imageanchor="1"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3e_TXrv6vl533e6dNw56vk5FaPfbIOAC1lKoPpdZwVGEHNHlny77k7w2qyanZnToLnpWuk88nXf11Oix-M73YrJAcsdCByETvHFuOyvD3DgNRMlGSo6OUHMTicumd0dQth4JaAGDHRpFD/s200/s_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRV2ZxMUZRdXNlaTQ">Multiple species in SBML Layout</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPoEAP7_udx0zp_h1J3xL6_6aKLuPEcMhlgwq3fawaU2x9gpJjFjiGzcJv87St57gm18d20QbysRlKrkyR-3xEscD8YIU43QtX-c0Y9xx16wus8yWmTy9SLxAONvbJD0_h4NQk8Lwl00xL/s1600/s_converted_converted.png" imageanchor="1"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPoEAP7_udx0zp_h1J3xL6_6aKLuPEcMhlgwq3fawaU2x9gpJjFjiGzcJv87St57gm18d20QbysRlKrkyR-3xEscD8YIU43QtX-c0Y9xx16wus8yWmTy9SLxAONvbJD0_h4NQk8Lwl00xL/s200/s_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRd2FoSV9YU0pxQlU">Multiple species converted</a></td>
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPklqePwqW5hLgDc83RIykw-5WC3X4AG21V3TwXn-PumVUNVQNiE84rh4z5iM5xNS_tdnw0U_urJEO1ulUZX9bMEBEGDEKOK7237DrZymcm0CEXBdK68lLuHB7ln97Vxs6GWJ7dReNFLGD/s1600/t_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPklqePwqW5hLgDc83RIykw-5WC3X4AG21V3TwXn-PumVUNVQNiE84rh4z5iM5xNS_tdnw0U_urJEO1ulUZX9bMEBEGDEKOK7237DrZymcm0CEXBdK68lLuHB7ln97Vxs6GWJ7dReNFLGD/s200/t_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVjdKMURVNjNmX00">Multiple species in SBML Layout with bezier</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3_CWwn1Uc7YgTLcxTSIpxs12Uy2SKfh3ejSA3Gc_Xy8yhrn5mCH8UPx4-YUYYdUSf5tHrv5LsMQPTaXWg3e2TuDb79iZsJ4gKzGqr_oBCRG4tS08kHZbltF7OOwapWR5eTEr7NzfTDU50/s1600/t_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3_CWwn1Uc7YgTLcxTSIpxs12Uy2SKfh3ejSA3Gc_Xy8yhrn5mCH8UPx4-YUYYdUSf5tHrv5LsMQPTaXWg3e2TuDb79iZsJ4gKzGqr_oBCRG4tS08kHZbltF7OOwapWR5eTEr7NzfTDU50/s200/t_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRODNTaTFVRmpBaTg">Multiple species with bezier converted
</a></td>
</tr>
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<td><a href="https://drive.google.com/open?id=0B7QYEhcLQncRODNTaTFVRmpBaTg"><br /></a></td>
<td></td>
</tr>
</tbody>
</table>
</div>
<div class="table-responsive">
While working on these conversions, I encountered two problems. First is defining bezier curve with one reactant and one product. Currently, I can only convert bezier curves only when there are multiple reactants and products like the second model above. I could not figure out a way to define a bezier curve in this situation. The second problem arises when the reaction contains the same species in both reactant and product. Every glyph is mapped to a unique SpeciesAnnotation. When working on the this kind of reaction both reactant and product were referencing the same species annotation. As a result, the output model would turn out as like the model below. To solve the second problem, I had to change up the main algorithm for conversion from SBML Layout to CellDesigner.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgu_fF1C2-3N0YR_9CPDrcLBjRg-P4eVnoGOEUFn4D7pF1PasyjFkRW_taU1k-qO5QYOpeEoNLVo6JuZaYT-SMCeTwDezJOtsUOmpP90YqnDoQDOvwmbR-H8PoHHfgOCC5Awv9NlPLyzZzG/s1600/unko.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgu_fF1C2-3N0YR_9CPDrcLBjRg-P4eVnoGOEUFn4D7pF1PasyjFkRW_taU1k-qO5QYOpeEoNLVo6JuZaYT-SMCeTwDezJOtsUOmpP90YqnDoQDOvwmbR-H8PoHHfgOCC5Awv9NlPLyzZzG/s200/unko.png" width="200" /></a></div>
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Model with same species as reactant and product</div>
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So, here is the chart for converting SBML Layout to CellDesigner Annotation. Blue means it's completed, red means it's not yet completed, green means it's unconvertable.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN-wVI4HeEIpiGSNusfTbtEnTHygaURc-hLLCLimzYrsGkusx0lplpkSyGya3bziJxn3Ekg7dQSK4VRi1ahq7czR0ZFOCT-6LM-iLWaDzWs6lfWWhvuSE8KDVHLYReg-upXda8pFp6rwHN/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN-wVI4HeEIpiGSNusfTbtEnTHygaURc-hLLCLimzYrsGkusx0lplpkSyGya3bziJxn3Ekg7dQSK4VRi1ahq7czR0ZFOCT-6LM-iLWaDzWs6lfWWhvuSE8KDVHLYReg-upXda8pFp6rwHN/s320/CellDesigner+Annotation.png" width="320" /></a></div>
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Since there is only 3 weeks left for GSoC, I have created a brief todo list. Each tasks are ordered in priority levels, where the highest priority task coming up top. From now on, I will be mostly following this list.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLEAvt4LHyRSPws8Nier_Uun3u-lPArRDdjAayJzPLmo5QVG6-y6VSoktL48HUmlAMzoyEqrw3qr9l1xwRtSFiiC0qyj-RzP2OJ8l7Fkcd7Upgh58U-PuIEsNhOPQ1Ly5iznvlext7a2H_/s1600/Todo+List.png" imageanchor="1"><img border="0" height="244" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLEAvt4LHyRSPws8Nier_Uun3u-lPArRDdjAayJzPLmo5QVG6-y6VSoktL48HUmlAMzoyEqrw3qr9l1xwRtSFiiC0qyj-RzP2OJ8l7Fkcd7Upgh58U-PuIEsNhOPQ1Ly5iznvlext7a2H_/s320/Todo+List.png" width="320" /></a></div>
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Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-48963148397837241672016-07-19T20:01:00.001-07:002016-08-20T01:13:29.857-07:00Week 12Hi all,<br />
<br />
This week, I have been a bit busy but I was able to start on converting the reactions. So far, the converter is able to convert simple reactions without any bending with modifiers.<br />
<br />
<br />
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<col class="col-xs-2"></col>
<col class="col-xs-2"></col>
</colgroup>
<tbody>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgPc8rUWY1Q7T-vqhyasVYY-VpU2g2LkBpC_Rv5bqsYzD_E9KqcQyyAA7oo0kfc_E_LjZLvzBFoEtCya1D-nXRrT_hMRsELORLXH6SgVB1obPzSGT_9lLPUIUkJW2y8giCDsMVHcSfCc_9/s1600/basic.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgPc8rUWY1Q7T-vqhyasVYY-VpU2g2LkBpC_Rv5bqsYzD_E9KqcQyyAA7oo0kfc_E_LjZLvzBFoEtCya1D-nXRrT_hMRsELORLXH6SgVB1obPzSGT_9lLPUIUkJW2y8giCDsMVHcSfCc_9/s200/basic.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRQ2JYanM1U1E5VzQ">Simple reaction original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6wLaEoe-S3cGiNJLUqfkyMDoULmXYtkD4PE_gXwlq-HHPkJk-GxaU8EjNfiuQiDhGs05qQVbrdMtgyATyEOOKfMo2o6iiqAwqNhHP5cjDt001rhOcP47C1JiG83YQcdjpg0dy0lRhivAO/s1600/basic_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6wLaEoe-S3cGiNJLUqfkyMDoULmXYtkD4PE_gXwlq-HHPkJk-GxaU8EjNfiuQiDhGs05qQVbrdMtgyATyEOOKfMo2o6iiqAwqNhHP5cjDt001rhOcP47C1JiG83YQcdjpg0dy0lRhivAO/s200/basic_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRaldrUVpjRlJMczQ">Simple reaction converted</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSIk02wrgGvXm-qk5AYyQMnwyEQNap2-YSzBndZfdBd-0Z6ZHonpP-EVo-Atr5FiBpmMX6lxjyGvW34GcpT_SoMxRqiLa8HsDX5iGtiJWBezrn08VpHHR9jtAmCgyrX3LGOHy7C-1LHoit/s1600/modifier.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSIk02wrgGvXm-qk5AYyQMnwyEQNap2-YSzBndZfdBd-0Z6ZHonpP-EVo-Atr5FiBpmMX6lxjyGvW34GcpT_SoMxRqiLa8HsDX5iGtiJWBezrn08VpHHR9jtAmCgyrX3LGOHy7C-1LHoit/s200/modifier.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRenNtdF9hTzlrUUU">Reaction with modifier original</a>
</td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrBjN46jKlhSu22no8BehtbwsG3R3xM857SB8Rpt3FTCRMzJ2-SiPuVFtQ20Wgu921B0ENDrOLvZCSFVyLX3JJLkZo1l_j3xNYzBRch9luIbJCSxbtc60YI22Ly5VJ376VKcdnvDoBh4Xs/s1600/modifier_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrBjN46jKlhSu22no8BehtbwsG3R3xM857SB8Rpt3FTCRMzJ2-SiPuVFtQ20Wgu921B0ENDrOLvZCSFVyLX3JJLkZo1l_j3xNYzBRch9luIbJCSxbtc60YI22Ly5VJ376VKcdnvDoBh4Xs/s200/modifier_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWWluSllUczczcUk">Reaction with modifier converted</a>
</td>
</tr>
</tbody>
</table>
</div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
The progress so far for converting the SBML Layout to CellDesigner is listed below. For next week, I will be starting on more complex reactions such as those with bezier curves or multiple line segments.</div>
<div class="table-responsive">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkFRZqxTY8B0oYMVgyd-Ihqi4nsKD1VZJbw0Xq_xYvNCka1q5AG9uEbU6byUHblqHfgyMRfCFkY5-FrEbu8jqzOWUciEpYL8tQUj-nBWoCGHvgj6354z1Rxwb5sRxXOGrRIOXbxOP_o5ZE/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkFRZqxTY8B0oYMVgyd-Ihqi4nsKD1VZJbw0Xq_xYvNCka1q5AG9uEbU6byUHblqHfgyMRfCFkY5-FrEbu8jqzOWUciEpYL8tQUj-nBWoCGHvgj6354z1Rxwb5sRxXOGrRIOXbxOP_o5ZE/s320/CellDesigner+Annotation.png" width="320" /></a></div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com2tag:blogger.com,1999:blog-7053847733245746410.post-77984169923463900532016-07-13T00:05:00.000-07:002016-08-20T01:13:20.749-07:00Week 11Hi all,<br />
<br />
For the previous 2 weeks, I have been trying to get the CellDesigner to read the converted model from SBML layout. This week, I have finally got some visual result. I can now open the converted model with CellDesigner.<br />
<table class="table table-bordered table-striped">
<colgroup>
<col class="col-xs-2"></col>
<col class="col-xs-2"></col>
</colgroup>
<tbody>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqnMVBPgKyNREsXhJSzChd2GB_SJwCnRjkYm2SeTl5hd3L_yvNyRBCEUw0p357u5o-voApiHf4u0jsWPm38Yr55ukXBuD9bxIthYK9fIOV9cz8y8Qwo7hvzJxYzy2-mDvkOJMXvPeduaTG/s1600/species_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqnMVBPgKyNREsXhJSzChd2GB_SJwCnRjkYm2SeTl5hd3L_yvNyRBCEUw0p357u5o-voApiHf4u0jsWPm38Yr55ukXBuD9bxIthYK9fIOV9cz8y8Qwo7hvzJxYzy2-mDvkOJMXvPeduaTG/s200/species_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUXp6LXJVclkxaWs">Species original</a></td><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1enOeAQRByozwq52yf31qRVuIExCufU_KVmbI5bvB1rfi_Uzw60SYzwhmh1ttaLTZl6X-Vm3og8X15f_uiZZJ6LvfTgGNkOEAsRhbGV2tyJpNlgK8Id0Nx1iaq4vLCJZqSsp0qGjKEap1/s1600/species_converted_converted.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1enOeAQRByozwq52yf31qRVuIExCufU_KVmbI5bvB1rfi_Uzw60SYzwhmh1ttaLTZl6X-Vm3og8X15f_uiZZJ6LvfTgGNkOEAsRhbGV2tyJpNlgK8Id0Nx1iaq4vLCJZqSsp0qGjKEap1/s200/species_converted_converted.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRek1jOVNCckhKbDg">Species converted</a></td>
</tr>
</tbody></table>
<br />
Here are the diagram on how much the conversion is completed. Blue means it's completed, red means it's not yet completed, green means it's unconvertable. After I convert the catalyzed reaction on species, I will start on the reaction conversion.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjaBw5kqDgRH5LiD9UtyZjA6diWArsrDcY_jHjDGSNk66zSXcCBMCz9c-RmHWxQVXHoMSl9nLRS3Zv8lHKXWAk44ZVDLzCTcvsxlwD5CSM_mTWjqgkVOEeTugdnHxI7w7TIcsH1jfxobAS/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjaBw5kqDgRH5LiD9UtyZjA6diWArsrDcY_jHjDGSNk66zSXcCBMCz9c-RmHWxQVXHoMSl9nLRS3Zv8lHKXWAk44ZVDLzCTcvsxlwD5CSM_mTWjqgkVOEeTugdnHxI7w7TIcsH1jfxobAS/s320/CellDesigner+Annotation.png" width="320" /></a><br />
<br />
<br />
<div>
<br />
Also, last week I found out that the math equation was converted incompletely when unmarshaled with JAXB. When converting SBML Layout to CellDesigner Annotation, the output model will be generated using JAXB having incomplete math equation. To overcome this problem, the converter will copy the math equations once the model is outputted with JAXB. The chart below shows the overview of the converter.<br />
<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdU8lTEczL1P_vuijiqMdcso1Ml4w38df9ezv7hL2SxwvPEBGTKPA0gRAgs-tqkPShVF0OTF1glGD9Gb6rzgk-BNoG-O9t4PEwPQcdepVhZbEeEz6_Nc-uW4AUgth42a6G4WyKh1U7Ak9T/s1600/algo.png" imageanchor="1"><img border="0" height="230" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdU8lTEczL1P_vuijiqMdcso1Ml4w38df9ezv7hL2SxwvPEBGTKPA0gRAgs-tqkPShVF0OTF1glGD9Gb6rzgk-BNoG-O9t4PEwPQcdepVhZbEeEz6_Nc-uW4AUgth42a6G4WyKh1U7Ak9T/s320/algo.png" width="320" /></a></div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-31195145765905493322016-07-06T02:31:00.000-07:002016-08-20T01:13:10.406-07:00Week 10Hello all,<br />
<br />
This week, I have been working on the actual conversion from SBML Layout to CellDesigner Annotation. I have started the conversions for species and compartment using the informations from their glyphs. The chart below shows how much I have covered so far for conversion. Blue means it's completed, red means it's not yet completed, green means it's unconvertable.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirNAg-yicA_5K9wVeGl1lTSP5GYbsKb-Gn15uekF4_eqRjctvPla6yJrpBdB2wfeguCV-eEyAIgpLtbR9yqKs2RGa82025VortNvWEVLryI9gEsdL9JpUTnbmw5gZ6Wn55sxZAo6l-KTTq/s1600/CellDesigner+Annotation.png" imageanchor="1"><img border="0" height="295" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirNAg-yicA_5K9wVeGl1lTSP5GYbsKb-Gn15uekF4_eqRjctvPla6yJrpBdB2wfeguCV-eEyAIgpLtbR9yqKs2RGa82025VortNvWEVLryI9gEsdL9JpUTnbmw5gZ6Wn55sxZAo6l-KTTq/s320/CellDesigner+Annotation.png" width="320" /></a><br />
<br />
<br />
Another thing I have been doing is that I have been creating a command line interface.<br />
<br />
git clone https://github.com/funasoul/celldesigner-parser<br />
mvn install<br />
java -jar celldesigner-parser-0.0.1-SNAPSHOT-jar-with-dependencies.jar input.xml [output.xml] [CD2Layout / Layout2CD]<br />
<br />
First create the runnable jar file with maven. Then run the jar with arguments input file, path to output (optional), and which direction CellDesigner to Layout or Layout to CellDesigner (optional).<br />
<br />
<br />
Also, I tried to provide a visual aid on the progress I have made, however CellDesigner can't read my converted model yet. Currently something is wrong with the Species Alias and throws an exception. For next week, my first goal is to get some graphical output on the converted model.<br />
<div>
<br />
Here are the result I get for my current implementation.<br />
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRb05HTmVvNkJXbEU">Layout model</a><br />
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRLXVfbWRfanJiaE0">CellDesigner Annotation Model</a><br />
<br />
<br />
<br />
One last thing. I have noticed an error when unmarshaling the SBML file. In the kinetic law, the math equation is converted in the wrong form.<br />
<br />
Original Model is written like on the below.<br />
<mathml:math><br />
<mathml:apply><br />
<mathml:times/><br />
<mathml:ci> k1 </mathml:ci><br />
<mathml:ci> s1 </mathml:ci><br />
</mathml:apply><br />
</mathml:math><br />
<div>
<br /></div>
<div>
When unmarshaled, the duplicating ci attribute is removed.</div>
<div>
<div>
<mathml:math></div>
<div>
<mathml:apply></div>
<div>
<mathml:ci> k1 </mathml:ci></div>
<div>
<mathml:times/></div>
<div>
</mathml:apply></div>
<div>
</mathml:math></div>
</div>
<div>
<br /></div>
<br />
So whenever I convert the model to SBML Layout to CellDesigner Annotation, it changes the equation. I presume something might be wrong with the MathML schema (sbml-mathml.xsd). </div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-66156875248019645212016-06-28T04:12:00.000-07:002016-06-29T07:01:51.740-07:00First week for converting Layout to CellDesigner AnnotationHello all,<br />
<br />
Last week, I have mentioned that there are still few attributes in the CellDesigner annotation to be converted. Before working the conversion for the other direction, I have implemented the conversions for links and bezier curves.<br />
<br />
<div class="table-responsive">
<table class="table table-bordered table-striped">
<colgroup>
<col class="col-xs-2"></col>
<col class="col-xs-2"></col>
</colgroup>
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<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjd9WxKDkv7Dvx-iQouHlRNchMIOfvNOfnod901m5gBRKX41B_1eN0G5uujP-ktBfykx3DzD96g0oxNQ80Gz10f8CqeuHEI90ZxhrcEk6nolSHdbGDLTZyXDWDMCqJEIDWGpGI3SvWWGz_S/s1600/CD_link.png" imageanchor="1"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjd9WxKDkv7Dvx-iQouHlRNchMIOfvNOfnod901m5gBRKX41B_1eN0G5uujP-ktBfykx3DzD96g0oxNQ80Gz10f8CqeuHEI90ZxhrcEk6nolSHdbGDLTZyXDWDMCqJEIDWGpGI3SvWWGz_S/s200/CD_link.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRRmNOMXdad3hwcm8">link original </a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEik136iWYdQmRWJRdWXWRMCPiyGQbzxfoWv8DgWY5YQj3K_S-Vjfz3BSOLGA8K436wngdqqyFa9Rbf08I_kfyesOFCLzA1wlMaZ_4ydm_aJezMXxIZJVrZccFVxwJnNWFcdNgLCB97E10Ze/s1600/link.png" imageanchor="1"><img border="0" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEik136iWYdQmRWJRdWXWRMCPiyGQbzxfoWv8DgWY5YQj3K_S-Vjfz3BSOLGA8K436wngdqqyFa9Rbf08I_kfyesOFCLzA1wlMaZ_4ydm_aJezMXxIZJVrZccFVxwJnNWFcdNgLCB97E10Ze/s200/link.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWFg1T1ZxUi1Dc1E">link converted</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbtltcuKaAv4s29E1-LuONUEB8uUz7Gu4cFjciDdWL-BaVsqXPY8qPQg03bLLEKofTfv1gMmfy1WTlTZkuhiFx94saRd95mbSqMCHWjh_9oIaP76zJxEJTPnfTphLCVOa-p8aYdJMmdpea/s1600/CD_bezier.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbtltcuKaAv4s29E1-LuONUEB8uUz7Gu4cFjciDdWL-BaVsqXPY8qPQg03bLLEKofTfv1gMmfy1WTlTZkuhiFx94saRd95mbSqMCHWjh_9oIaP76zJxEJTPnfTphLCVOa-p8aYdJMmdpea/s200/CD_bezier.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUklCN0ppckpyR1U">bezier original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHU9SFOH8M3f5vXyNCxRc6Dih1Ak5US8170vSV1_6hkSZ2FxkOi_ZZeA72I3g4LHKDy8r2aBr-l9EduTgVNA7JqcDajwDqZaz-A2vJE0arON-NQ2B7WvtSMO9fQ9c2S9ErDjGJ4y44YpFM/s1600/bezier.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHU9SFOH8M3f5vXyNCxRc6Dih1Ak5US8170vSV1_6hkSZ2FxkOi_ZZeA72I3g4LHKDy8r2aBr-l9EduTgVNA7JqcDajwDqZaz-A2vJE0arON-NQ2B7WvtSMO9fQ9c2S9ErDjGJ4y44YpFM/s200/bezier.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNWdJX2s2LUEzbk0">bezier converted</a></td>
</tr>
</tbody>
</table>
</div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
As for the conversion of SBML Layout to CellDesigner Annotation, I have been working on the APIs for SBML objects such as Species and for inputs/outputs. The basic algorithm for the conversions with be as follow.</div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
<ol>
<li>Read model with JSBML</li>
<li>Downgrade 1. to Level 2 Version 4</li>
<li>Unmarshal 2. as string</li>
<li>From 1. convert the Layout attributes to 3.</li>
</ol>
<div>
So far, I have created the basic algorithms above and have created model with empty CellDesigner annotation. Below are the progress I have made so far. For next week, I will be starting on converting each type of glyphs.</div>
</div>
<div class="table-responsive">
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVGhPc01pcENwRFk">Layout Model</a><br />
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNFlLTUhJb0xNcTQ">Converted Model</a></div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
<br /></div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-3839406662394281752016-06-22T02:19:00.000-07:002016-06-29T07:03:19.105-07:00Half way throughHello all,<br />
<br />
This week is midterm evaluation week. Which means that I am half way through the GSoC program. This week, I have been working on the conversion of complex species and edit points for branched reactions.<br />
<br />
<br />
<div class="table-responsive">
<table class="table table-bordered table-striped">
<colgroup>
<col class="col-xs-2"></col>
<col class="col-xs-2"></col>
</colgroup>
<tbody>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqoGNoJFbbwSLwcINPmQIe1evBTNnSNMHm6mTX3LPPcDHp3VTEM0qOdcLL1yuf-OHyIwKqmETYijp-VrwjgU09tABCOH5Ee21p90p4wpOKQY9-WOX67PjIU0DBnXmwoPkCU5QPV2RVARaL/s1600/CD_complex.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqoGNoJFbbwSLwcINPmQIe1evBTNnSNMHm6mTX3LPPcDHp3VTEM0qOdcLL1yuf-OHyIwKqmETYijp-VrwjgU09tABCOH5Ee21p90p4wpOKQY9-WOX67PjIU0DBnXmwoPkCU5QPV2RVARaL/s200/CD_complex.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVzhhYzFBTERGNE0">complex original 1</a></td><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1RTzyLsrqdkc9vgH8-doQZJ1tRQ0sjF7ihs4oKRbu7e7r3Y-pWchtH3983swq43YZqmy5x00CIRQ2bB0JpgPa_AsnnVT2Gc9Wi3J_VLjc13ZR487mj9E47wlaNQgKUu5AncYbhu6F5mIf/s1600/complex.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1RTzyLsrqdkc9vgH8-doQZJ1tRQ0sjF7ihs4oKRbu7e7r3Y-pWchtH3983swq43YZqmy5x00CIRQ2bB0JpgPa_AsnnVT2Gc9Wi3J_VLjc13ZR487mj9E47wlaNQgKUu5AncYbhu6F5mIf/s200/complex.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRMUlkRm5ka0ZLWkk">complex converted 1</a></td></tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7MrgweBtF9cWXUKh49utNC8G8n4NGu2H5wC69s2IDG2fp_zz76LZ7rDw9kZuDnLJ0iD7PVKXJ2kFcWnNANK8cueVdhzo5jswhMBN6NEy1BxuesE-xCpcQ8Ltd2Eu-_NzFg9yTuOcVCCda/s1600/CD_complex2.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7MrgweBtF9cWXUKh49utNC8G8n4NGu2H5wC69s2IDG2fp_zz76LZ7rDw9kZuDnLJ0iD7PVKXJ2kFcWnNANK8cueVdhzo5jswhMBN6NEy1BxuesE-xCpcQ8Ltd2Eu-_NzFg9yTuOcVCCda/s200/CD_complex2.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRaGxQS0VtMGllbW8">complex original 2</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgq5Epiasp-9jlSCKWMR6IhU50RVHuOcXWLoG9TthT1_jhuCsjYD3xF4jPsmWmftMcg30-QNVD8Mhb_slLKBU8XIEXOxLr_atnHG3Mj70I399yvAc5D8_sTeuLmNGk-TOxDg8Kd3McyQa6x/s1600/complex2.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgq5Epiasp-9jlSCKWMR6IhU50RVHuOcXWLoG9TthT1_jhuCsjYD3xF4jPsmWmftMcg30-QNVD8Mhb_slLKBU8XIEXOxLr_atnHG3Mj70I399yvAc5D8_sTeuLmNGk-TOxDg8Kd3McyQa6x/s200/complex2.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRZV8xZkxIN2Z3OTQ">complex converted 2</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg18IAQbyZN3GCer0H0QuP1ZZuMavuiTfruxQVbF7tG_EnC6DJ9A4hX7uORIv64U24msZerdevacmNUwepu4iv73D_-FExfDvda3z7AiwBJVOJ00pHTnUZb4r9-WidsYhY8R3SPl_odagg6/s1600/CD_dissociation.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg18IAQbyZN3GCer0H0QuP1ZZuMavuiTfruxQVbF7tG_EnC6DJ9A4hX7uORIv64U24msZerdevacmNUwepu4iv73D_-FExfDvda3z7AiwBJVOJ00pHTnUZb4r9-WidsYhY8R3SPl_odagg6/s200/CD_dissociation.png" width="200" /></a> <br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRM09Id0lraVRDbFU">branched original 1</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmE6EP1YyVBEtOEYLgqtg22lJPieqyiByULaJWJn5HcO35lDKFIhDVNmmrhR-OCyFv1ZLcxQava7VtrRnw0AMW971wyYnwYVoVgbnVdpUQayRaT8Vx8yiPdyr8EBKVdjgwEXSRqzzFptLr/s1600/dissociation.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmE6EP1YyVBEtOEYLgqtg22lJPieqyiByULaJWJn5HcO35lDKFIhDVNmmrhR-OCyFv1ZLcxQava7VtrRnw0AMW971wyYnwYVoVgbnVdpUQayRaT8Vx8yiPdyr8EBKVdjgwEXSRqzzFptLr/s200/dissociation.png" width="200" /></a>
<br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWkdtaktDZllsZUE">branched converted 1</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipv9o4IPE-Uw5xFhF-UX0IlJaJBsYkzZuzdyGUNTdy_FhcmKc8DizJm41cueZiLIeOIo2hLK0P5l5DsDxZnfk1QA2H2XBYpGqCVDGeCSzd81x6YoJnInKG_6d6SBgWdJXCFi9zJFuA8LD-/s1600/CD_heterodimer.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEipv9o4IPE-Uw5xFhF-UX0IlJaJBsYkzZuzdyGUNTdy_FhcmKc8DizJm41cueZiLIeOIo2hLK0P5l5DsDxZnfk1QA2H2XBYpGqCVDGeCSzd81x6YoJnInKG_6d6SBgWdJXCFi9zJFuA8LD-/s200/CD_heterodimer.png" width="200" /></a> <br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRMlRjdHRYYVdwVnM">branched original 2</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNpn6dggtPZAVDAw1PzND8casEWrHYat6cW0ScK89lyE4y0acqiG89mN2LeA55bIqa6ANUwEjE8jzdShthiC-JETtTtnzk8FvcN9Sfwmw6SAwamj_jcLb_IeDW5JYFwRWuk0s4b5gOmgYA/s1600/heterodimer.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNpn6dggtPZAVDAw1PzND8casEWrHYat6cW0ScK89lyE4y0acqiG89mN2LeA55bIqa6ANUwEjE8jzdShthiC-JETtTtnzk8FvcN9Sfwmw6SAwamj_jcLb_IeDW5JYFwRWuk0s4b5gOmgYA/s200/heterodimer.png" width="200" /></a><a href="https://drive.google.com/open?id=0B7QYEhcLQncRUGhUdTNkdHNLY2M"> </a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUGhUdTNkdHNLY2M">branched converted 2</a></td>
</tr>
</tbody>
</table>
</div>
<div class="table-responsive">
<br /></div>
<div class="table-responsive">
Since it's midterm week, I have created a diagram to show how much of the conversion from CellDesigner Annotation to SBML layout has been completed. All items in blue are the ones that have been covered and are able to convert. Items in red are annotations that have not yet been implemented. From this diagram, you can tell that I still need to work with reactant / product links, residues, beziers, and boolean. </div>
<div class="table-responsive">
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<div class="table-responsive">
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<iframe height="480" src="https://drive.google.com/file/d/0B7QYEhcLQncRU2F4VFM2SVNXNzA/preview" width="640"></iframe>
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For my initial plan, I had my midterm goal set as completing the conversion of CellDesigner Annotation to SBML Layout. The converter still have some missing features, but I have roughly accomplished my goal. As for my next goal, I will be working on the conversion from SBML Layout to CellDesigner Annotation and will have a converter that converts both ways.<br />
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<br />Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-68625107550326010292016-06-14T07:13:00.001-07:002016-06-14T21:48:44.453-07:00Hello everyone,<br />
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Since last week, I have been working with the conversion of reactions. This week, I have been mainly working on edit points (reaction with bending lines) and modifiers. Here are some diagrams that I have accomplished .<br />
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<div class="table-responsive">
<table class="table table-bordered table-striped" style="text-align: center;">
<colgroup>
<col class="col-xs-2"></col>
<col class="col-xs-2"></col>
</colgroup>
<tbody>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdHuTcWZuR79vDi3Crf9Mc32BKyDqupk6yMUhK3pluXr6K8hz6hhKfYIam7ZnfmMZkciFUFwqe7YdT1tEgWb7NgGnZmw-9dDzDGmtZns0dT2xWf64QAMbqzZj8O_WUBa0yF1Id72Bxxf6b/s1600/anchor2.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdHuTcWZuR79vDi3Crf9Mc32BKyDqupk6yMUhK3pluXr6K8hz6hhKfYIam7ZnfmMZkciFUFwqe7YdT1tEgWb7NgGnZmw-9dDzDGmtZns0dT2xWf64QAMbqzZj8O_WUBa0yF1Id72Bxxf6b/s200/anchor2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRMVpiaXJCVnN2Q3M">simple anchor model original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxCfN0HVZuqIJudt1lbIyTTQlImksV1J1mHp7Am_tPUhg4zt10H7jUwuAYXpKqwpa9x04lhEv2mG8DfKhB8y7cjI3uExDLhWRE1ibwz_z4ez1xXUsvYdgbj9XTDC3-ely5rJh4tebG4BVB/s1600/CD_anchor2.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxCfN0HVZuqIJudt1lbIyTTQlImksV1J1mHp7Am_tPUhg4zt10H7jUwuAYXpKqwpa9x04lhEv2mG8DfKhB8y7cjI3uExDLhWRE1ibwz_z4ez1xXUsvYdgbj9XTDC3-ely5rJh4tebG4BVB/s200/CD_anchor2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRRmJwOEZZOVdpeHc">simple anchor model converted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgapK2TweQ6ove4bkvaE69p7UTvs9Pz97rpKdjsu0vWqdNqLwvpdIZYoOGsfdJZryjO2ewGiTZScTraAAJ-Q_FzmHYuiHHJTZ107F-i6x2fJizjGI05bQT1wL-1thOuXXoWJEo6vgBCsBG/s1600/anchor3.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgapK2TweQ6ove4bkvaE69p7UTvs9Pz97rpKdjsu0vWqdNqLwvpdIZYoOGsfdJZryjO2ewGiTZScTraAAJ-Q_FzmHYuiHHJTZ107F-i6x2fJizjGI05bQT1wL-1thOuXXoWJEo6vgBCsBG/s200/anchor3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUm1ZeGFXdV9iN1E">simple anchor model 2 original </a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGRITBnKKNa10nG2gThrJ2J1D3Aa-tgsR-PPQ8MuAtVpMs0B7i3GymfcrsZPa83Ug0JNI65BKXw9qHuxpr6cXMyeCm_jKzagjrRVr_A2rbvK3xAIc_Ks7IGSvFcdNwboTb6KOSj7yCIX3z/s1600/CD_anchor3.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGRITBnKKNa10nG2gThrJ2J1D3Aa-tgsR-PPQ8MuAtVpMs0B7i3GymfcrsZPa83Ug0JNI65BKXw9qHuxpr6cXMyeCm_jKzagjrRVr_A2rbvK3xAIc_Ks7IGSvFcdNwboTb6KOSj7yCIX3z/s200/CD_anchor3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUjdVQUN1RmlPcUE">simple anchor model 2 converted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHvkMNKQh4zTEOf4cGZD_joTpeTE399iG8LU3h9BjLRi0ZrM4n30jlSulKheO4G9OE_QRCcbaOKz20cgU1TssaMdfEPC0RBoiHCxoM7BhjMjPRspOrwz_xumqNRI-MBNMMPfAP18OTrAXc/s1600/anchor4.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHvkMNKQh4zTEOf4cGZD_joTpeTE399iG8LU3h9BjLRi0ZrM4n30jlSulKheO4G9OE_QRCcbaOKz20cgU1TssaMdfEPC0RBoiHCxoM7BhjMjPRspOrwz_xumqNRI-MBNMMPfAP18OTrAXc/s200/anchor4.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRSWV0SERjREJla2M">simple anchor model 3 original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-gj1yyGzwiPgVQ80DPmyGQpf-YtEkNBgz431__4_l1WCB1HWti2GUe8MTJPx6eftV-Rg9xLj8SVxj3rLF5RudaF7QUXBjx8ZviYbvh16SasWTVMGMeGEFHsdZVsG9oXZ9oIki9-sotpkC/s1600/CD_anchor4.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-gj1yyGzwiPgVQ80DPmyGQpf-YtEkNBgz431__4_l1WCB1HWti2GUe8MTJPx6eftV-Rg9xLj8SVxj3rLF5RudaF7QUXBjx8ZviYbvh16SasWTVMGMeGEFHsdZVsG9oXZ9oIki9-sotpkC/s200/CD_anchor4.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRdVN1RmY1c2Roblk">s</a><a href="https://drive.google.com/open?id=0B7QYEhcLQncRdVN1RmY1c2Roblk">imple anchor model 3 converted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6PghcN6s5BjsJPgglYFbtAm2p0suFVbg4KLoJeZ9QTKfqwilp4iuQkIScVqVai_sB1s3ZBpqZDQ5TRkro6gdGr_VZ_2_cAaGMMjSLWXqXyZVnxstO78eNE6QWjbC-hlgf73br8ZJpdSx7/s1600/anchor5.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6PghcN6s5BjsJPgglYFbtAm2p0suFVbg4KLoJeZ9QTKfqwilp4iuQkIScVqVai_sB1s3ZBpqZDQ5TRkro6gdGr_VZ_2_cAaGMMjSLWXqXyZVnxstO78eNE6QWjbC-hlgf73br8ZJpdSx7/s200/anchor5.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRQmh6Q3NBX0toNFE">simple anchor model 4 original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRm2qMiWtvYPZBUZyCYFKMvRnVWIx8nqf2cchHoF_gUpMiqwnTAb33PSjrg5JmImtKPMqjm8wOOxMQIYOXQYQEUT9ogbdbHNNPxFm0C1uNxYVdnLAs4sZT27em797VEcZghTnh5h-uexN8/s1600/CD_anchor5.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRm2qMiWtvYPZBUZyCYFKMvRnVWIx8nqf2cchHoF_gUpMiqwnTAb33PSjrg5JmImtKPMqjm8wOOxMQIYOXQYQEUT9ogbdbHNNPxFm0C1uNxYVdnLAs4sZT27em797VEcZghTnh5h-uexN8/s200/CD_anchor5.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNDB4dkRZRjFnQWs">simple anchor model 4 coverted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-uovc7oBySysc_vjswKHaHX_PVCn1M3xPSTZcFHpVUmFY2BdNt0ewj-O1ZE2XCALUVqJHRVRbv-koVmB4Ln79wRzJ059KgcV0USF8qhk5BNTF3omsEqoTHpHYL_ui119UXgYQ9xUIi_-Z/s1600/an.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-uovc7oBySysc_vjswKHaHX_PVCn1M3xPSTZcFHpVUmFY2BdNt0ewj-O1ZE2XCALUVqJHRVRbv-koVmB4Ln79wRzJ059KgcV0USF8qhk5BNTF3omsEqoTHpHYL_ui119UXgYQ9xUIi_-Z/s200/an.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNENwM2ZyV01qQ3c">anchor model original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYla9TlmBMsdglFh9yrEfsM7NGGbmRdzSC53aL_NKTLo6xKCPuQKJ8Cfe6XAMUGwD-J3njNFXBNI7Yvy5h1rYD7KW6W50b4UOd45M09f0FKGyj_mZFFnvwpb7YclbjkmjtEWFuPwV5wxsI/s1600/CD_an.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYla9TlmBMsdglFh9yrEfsM7NGGbmRdzSC53aL_NKTLo6xKCPuQKJ8Cfe6XAMUGwD-J3njNFXBNI7Yvy5h1rYD7KW6W50b4UOd45M09f0FKGyj_mZFFnvwpb7YclbjkmjtEWFuPwV5wxsI/s200/CD_an.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncROVNmUk8zc2xRUHM">anchor model converted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7X5_s82Kd28_zlYVqQr6IURdMaiO59vabZIlyALkX-5L_LTkAwIKdHpG0inHwT3aHeBeyvZE3C6W1iwa8BxVMf8f4Hwg9SaNkwh7o3FNmpx61Y2nXvONZPIYhnYR-m0Ke4b1wpI0J5OlU/s1600/an2.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7X5_s82Kd28_zlYVqQr6IURdMaiO59vabZIlyALkX-5L_LTkAwIKdHpG0inHwT3aHeBeyvZE3C6W1iwa8BxVMf8f4Hwg9SaNkwh7o3FNmpx61Y2nXvONZPIYhnYR-m0Ke4b1wpI0J5OlU/s200/an2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRVUZub1pzSWlBX0U">anchor model 2 original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKsHOPd-_TVhUV-CTIKn9QNBT3oEALLOyhy3NpCODSXFZlM12jp6SoK9wZE8Cnj-QdAjtzrf-hDhiyHaijbb3QpuTRKE9JptEiarWD5KVJrhiXd4TdNnQFzwSAom0WmGUXBbT8W4R7UBvi/s1600/CD_an2.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKsHOPd-_TVhUV-CTIKn9QNBT3oEALLOyhy3NpCODSXFZlM12jp6SoK9wZE8Cnj-QdAjtzrf-hDhiyHaijbb3QpuTRKE9JptEiarWD5KVJrhiXd4TdNnQFzwSAom0WmGUXBbT8W4R7UBvi/s200/CD_an2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRYUdiSWh0RDQ5Tk0">anchor model 2 converted</a></div>
</td>
</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUaQFwsO9gVi7Ih5MtecY8wqvi9WrMjvOLI2EdG2V121TLN1jCT4dc213RLju024q8geNnSqg-MKHKCd508ZHFff8wtRqk-xZ7hbAXj4JDt6AFFBlEpnabg12DNCGscAEph4IGEH_lA4qO/s1600/an3.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUaQFwsO9gVi7Ih5MtecY8wqvi9WrMjvOLI2EdG2V121TLN1jCT4dc213RLju024q8geNnSqg-MKHKCd508ZHFff8wtRqk-xZ7hbAXj4JDt6AFFBlEpnabg12DNCGscAEph4IGEH_lA4qO/s200/an3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRbEZvNmUyOUdHR1U">anchor model 3 original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIdwhVPGHxJS0YEa-H3fBmRqUCJEDFtlZIbnTd7WChTc0EzHuyaEDNlDKn9Uk2swVXiZ6RvQsmdH-eryCtTH3RtQsjJ3iI5W1oQuDIiJXO-vCPtw2UaOB5rb5jG_u_XGzYvDuR6vyfwW17/s1600/CD_an3.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIdwhVPGHxJS0YEa-H3fBmRqUCJEDFtlZIbnTd7WChTc0EzHuyaEDNlDKn9Uk2swVXiZ6RvQsmdH-eryCtTH3RtQsjJ3iI5W1oQuDIiJXO-vCPtw2UaOB5rb5jG_u_XGzYvDuR6vyfwW17/s200/CD_an3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRaWFSVUFLZjAzTm8">anchor model 3 converted</a></div>
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</tr>
<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhu93mXIdctdZD49ltvEWi6B5VinMJ0lak6tApiDLoteNQLGy1tErsOHj6M6y4IwCCxoll1fb8OHJSxLgohgXzt9Fm-kN6Qmr5F0KnjXRIZDOROEoqC06X_lx4bCGimyaoh9a6RY8NTPllf/s1600/catalysis.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhu93mXIdctdZD49ltvEWi6B5VinMJ0lak6tApiDLoteNQLGy1tErsOHj6M6y4IwCCxoll1fb8OHJSxLgohgXzt9Fm-kN6Qmr5F0KnjXRIZDOROEoqC06X_lx4bCGimyaoh9a6RY8NTPllf/s200/catalysis.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRX1hUUlZGSUJqejA">modifier model 1 original</a> (inhibition)</div>
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<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidhhIJbvM5V2hA0e8Qu8t4-5WqS2nYZAxtH4J9WwwxpuAis5ElYJ7VX78n_a86vwUNZ0Qm8aJrz2LIE0PrbIRIxT0QIJuLFC1udcO0W5d9q7t5cRbmCxBZ45c-LZEH0kFrxZndqibFXnap/s1600/CD_catalysis.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidhhIJbvM5V2hA0e8Qu8t4-5WqS2nYZAxtH4J9WwwxpuAis5ElYJ7VX78n_a86vwUNZ0Qm8aJrz2LIE0PrbIRIxT0QIJuLFC1udcO0W5d9q7t5cRbmCxBZ45c-LZEH0kFrxZndqibFXnap/s200/CD_catalysis.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRTkgybXVvamxPTGs">modifier model 1 converted</a> (inihibition)</div>
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<tr>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGgVcZTH5buJ_fJ0ifBtBjAbxljQiqfLlHUKx0zsw-OQ-Wf5UrKH9S-Q426MSpiYB4AjoPdZvUUp-Oavmr-x60tM-LeLsuQwO6QAJlQnMKr9WeqTMXomr9gIO5x1rlX5MFFRSGQ-4m6n1G/s1600/catalysis2.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGgVcZTH5buJ_fJ0ifBtBjAbxljQiqfLlHUKx0zsw-OQ-Wf5UrKH9S-Q426MSpiYB4AjoPdZvUUp-Oavmr-x60tM-LeLsuQwO6QAJlQnMKr9WeqTMXomr9gIO5x1rlX5MFFRSGQ-4m6n1G/s200/catalysis2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRWEsxLWs4ZUFodjA">modifier model 2 original</a></div>
</td>
<td><div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWP1lr6Ylnewt9Np0Gfd_mek8zCkBfcVTr97GDXUAGIqRouSIYhdBf1I6LZC6uZMlJ8jC4YzQ-S9jd7-a9xLRAq15_2eJlenJC01UXOK9W4M4Wkl8OWy1lxrWTcSd8i59jlF1sHXMxFzoi/s1600/CD_catalysis2.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWP1lr6Ylnewt9Np0Gfd_mek8zCkBfcVTr97GDXUAGIqRouSIYhdBf1I6LZC6uZMlJ8jC4YzQ-S9jd7-a9xLRAq15_2eJlenJC01UXOK9W4M4Wkl8OWy1lxrWTcSd8i59jlF1sHXMxFzoi/s200/CD_catalysis2.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNEhZOVZWUnloTkU">modifier model 2 converted</a></div>
</td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEie2wM5dzsU1oT5rNwcGcrSytqH5N6_jusJBxDkJZIGRBPAQdZ-_DfUQomtESi_M06sQ9U2m_4lR3nkyi8uJjL4FoHv_MlddgCh4tsE043YmRApxEddz1SQwdEyKcbTpY1ZbddSNxIwCzy2/s1600/catalysis3.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEie2wM5dzsU1oT5rNwcGcrSytqH5N6_jusJBxDkJZIGRBPAQdZ-_DfUQomtESi_M06sQ9U2m_4lR3nkyi8uJjL4FoHv_MlddgCh4tsE043YmRApxEddz1SQwdEyKcbTpY1ZbddSNxIwCzy2/s200/catalysis3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRNS1xNU9Udi1hSHM">modifier model 3 original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhidXk6gYQYHZbGFA366butNb8HsffUqE3UfFtfdGCBPxVMn_EG4fOPLHGEad0_EwwtIfzW-IGY7kyL4xkt_gJJTGcQAqpa280KSkZLVkYbOn8T7kMfC0DjiY2mok75zKMEB0UnDmAI9Ipn/s1600/CD_catalysis3.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhidXk6gYQYHZbGFA366butNb8HsffUqE3UfFtfdGCBPxVMn_EG4fOPLHGEad0_EwwtIfzW-IGY7kyL4xkt_gJJTGcQAqpa280KSkZLVkYbOn8T7kMfC0DjiY2mok75zKMEB0UnDmAI9Ipn/s200/CD_catalysis3.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRQ0docDB2V3YtUzg">modifier model 3 converted</a></td>
</tr>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2_g5lYgXss1rsYcDbIEkfpaAjqaTX3lkLaPv3tnleP5fxt9dCRdQpBEoe1B1ZszXAbHcK60sBTNZc6PrETCCzr4bR63DSZNopTZN2gTlTrYOwZt4JJq2sXxfTlU3lUsG-XXwErT9U9c-I/s1600/cat.png" imageanchor="1"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2_g5lYgXss1rsYcDbIEkfpaAjqaTX3lkLaPv3tnleP5fxt9dCRdQpBEoe1B1ZszXAbHcK60sBTNZc6PrETCCzr4bR63DSZNopTZN2gTlTrYOwZt4JJq2sXxfTlU3lUsG-XXwErT9U9c-I/s200/cat.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRZjVnc25vdE9wQUk">modifier model 4 original</a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTxm4uKNw-67Vm134ufELuhl-qgnWRog_89YURngbyT7R2xzlqkj7Hj7x0SyrZC-QhOAZxHbwQqzju1xQ2NLCdpnaimzeK2I9YmH3d0JC1KSJdSFOTQVGCs8J1eUMJGz4pqndsHpHRzFCD/s1600/CD_cat.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTxm4uKNw-67Vm134ufELuhl-qgnWRog_89YURngbyT7R2xzlqkj7Hj7x0SyrZC-QhOAZxHbwQqzju1xQ2NLCdpnaimzeK2I9YmH3d0JC1KSJdSFOTQVGCs8J1eUMJGz4pqndsHpHRzFCD/s200/CD_cat.png" width="200" /></a><br />
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRQ0lkbjJuZnlEckU">modifier model 4 converted</a></td>
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</tbody>
</table>
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For next week, I will continue working on the conversion of reaction. Heterodimers, dissociation, and truncation reaction with edit points, species complex, bezier curves, and residue are the things left to be completed. And since it is midterm evaluation next week, I am hoping to complete the CellDesigner annotation conversion to SBML Layout by then.</div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-23552531089247924852016-06-08T01:51:00.001-07:002016-06-14T21:24:53.369-07:00Hi everyone,<br />
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Last week, I have successfully converted the compartment and species from CellDesigner annotation to SBML Layout. Since then, I have been working on converting the reaction. So far, I have partial completed converting reaction.<br />
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For now, I have completed conversions reactions with straight lines and heterodimer association, dissociation. and truncation. Below are some of the models I have successfully converted.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKZNyH0tXziNLAiSvuj0UwfGYZv4Hqz9qtz_4k-btGRP13-h1o2NaxTAxPyP_8Hh9I-FCTQkVIXHBKrlPybfghv6Blj73OjKx3_ijxnw62eYoBzU5GiisbfGP53aFLSYDqct-V_P-Cb-xa/s1600/r1.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKZNyH0tXziNLAiSvuj0UwfGYZv4Hqz9qtz_4k-btGRP13-h1o2NaxTAxPyP_8Hh9I-FCTQkVIXHBKrlPybfghv6Blj73OjKx3_ijxnw62eYoBzU5GiisbfGP53aFLSYDqct-V_P-Cb-xa/s200/r1.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZdR9YiX34hNDtFg7_ZJkhd9P4fkfnzteCJWPNJBv2Rkgy3nDP4B81E7J_q89EwvYPiEvrzRfFEHXUBNtE3Y0IMKahonH1BdydZEfYrhcG98Bm1rI5oPiwEB96olkR6Ug4wnZL-KPum5uN/s1600/r1_CD.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZdR9YiX34hNDtFg7_ZJkhd9P4fkfnzteCJWPNJBv2Rkgy3nDP4B81E7J_q89EwvYPiEvrzRfFEHXUBNtE3Y0IMKahonH1BdydZEfYrhcG98Bm1rI5oPiwEB96olkR6Ug4wnZL-KPum5uN/s200/r1_CD.png" width="200" /></a></div>
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncReUtoUk95Q3FOeFU">original model 1 </a> <a href="https://drive.google.com/file/d/0B7QYEhcLQncReWhrTlI5M0xibHM/view?usp=sharing">converted model 1</a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwwuepOUynxjSu_DhGoyF-2xrQqFLnl9v9YFgUBad3170GDlqdhIXpmqfW1y3f2KggvrPle_vd2Gl509ouqtq9SPGmFcCpTRqJ1DmODgXhDwP6D3BR0MHM1Iw_LYKxuJTiXhVMLM1q0s1z/s1600/r2_CD.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwwuepOUynxjSu_DhGoyF-2xrQqFLnl9v9YFgUBad3170GDlqdhIXpmqfW1y3f2KggvrPle_vd2Gl509ouqtq9SPGmFcCpTRqJ1DmODgXhDwP6D3BR0MHM1Iw_LYKxuJTiXhVMLM1q0s1z/s200/r2_CD.png" width="200" /></a></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwwuepOUynxjSu_DhGoyF-2xrQqFLnl9v9YFgUBad3170GDlqdhIXpmqfW1y3f2KggvrPle_vd2Gl509ouqtq9SPGmFcCpTRqJ1DmODgXhDwP6D3BR0MHM1Iw_LYKxuJTiXhVMLM1q0s1z/s1600/r2_CD.png" imageanchor="1"></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcdWtPxpqyG4ZYk5U5Gjlb5YMeQO_cJabfhUAHyggrqawW_MjkhP-lFAGN9j4GeKJ4G-1CP3ofGC8w3-6xWBlV2bJ4VIpER2pgeior020O3M18S6uXNRCNznRKOd2sXG-z_ytyZPltvyR3/s1600/r2.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcdWtPxpqyG4ZYk5U5Gjlb5YMeQO_cJabfhUAHyggrqawW_MjkhP-lFAGN9j4GeKJ4G-1CP3ofGC8w3-6xWBlV2bJ4VIpER2pgeior020O3M18S6uXNRCNznRKOd2sXG-z_ytyZPltvyR3/s200/r2.png" width="200" /></a><br />
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncRUDFLVHBmMTB3VHc">original model 2 </a> <a href="https://drive.google.com/open?id=0B7QYEhcLQncRdm5MOXNBSlBnU2c"> converted model 2</a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeDeXwQEstvv8AkzTZrL_6Ac_gYgBzuG3BDhxLtSSrcbR5HIFYrQV4WK1MmfqHGLGZCZytuxT0eIjtI9L3FEhKjKC4b_pZZg1AMsWQcUhbhJEfwHzkWbgUuw1V4Wnlb-JGWXkZ8mmeg58C/s1600/heterodimer_CD.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeDeXwQEstvv8AkzTZrL_6Ac_gYgBzuG3BDhxLtSSrcbR5HIFYrQV4WK1MmfqHGLGZCZytuxT0eIjtI9L3FEhKjKC4b_pZZg1AMsWQcUhbhJEfwHzkWbgUuw1V4Wnlb-JGWXkZ8mmeg58C/s200/heterodimer_CD.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmv26DayrM88Ao3zl0_K93-G1PmCwYQzSs5pG4kcFKjLy3nZWsMUwKYZxE0wX_4ahIdrIpjsOBInfkghfke-4uwqM-jwx5gY_ofaaLfqNm4PFRaP9T4Q1tGWort3Vw5-fDVUEQFHYaGXqr/s1600/heterodimer.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmv26DayrM88Ao3zl0_K93-G1PmCwYQzSs5pG4kcFKjLy3nZWsMUwKYZxE0wX_4ahIdrIpjsOBInfkghfke-4uwqM-jwx5gY_ofaaLfqNm4PFRaP9T4Q1tGWort3Vw5-fDVUEQFHYaGXqr/s200/heterodimer.png" width="200" /></a></div>
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncReGMwMVhLaVZiX0k">heterodimer original</a> <a href="https://drive.google.com/open?id=0B7QYEhcLQncRUXZhVUhfc3E4SXM">heterodimer converted</a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYw3ooUCa7qoXjond4UHvFsCqhqAlqCOAb2eKxRQzljvfeD_FdKt9aV87KGGJIpTMADfR-BppCBjPo88i3BLo53KdsxIi_FEUEM1HIylENR_-y0wzFYTj9E-KvqOrIG3K7yq8N7HeY0UXV/s1600/dissociation._CD.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYw3ooUCa7qoXjond4UHvFsCqhqAlqCOAb2eKxRQzljvfeD_FdKt9aV87KGGJIpTMADfR-BppCBjPo88i3BLo53KdsxIi_FEUEM1HIylENR_-y0wzFYTj9E-KvqOrIG3K7yq8N7HeY0UXV/s200/dissociation._CD.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgLlfZcyFm-A4AAYI2ondQFkNx_ihWT0AT6-xMlsAPBo484D_WlQEW32JuA9FD_HCiOx8OA7vXFV9fEk5HcMHuY4rr0tUew11fUGaqUcqA4IjASgd4GTKhI1TkiY9ronPchMQGYtS9IU66/s1600/dissociation.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgLlfZcyFm-A4AAYI2ondQFkNx_ihWT0AT6-xMlsAPBo484D_WlQEW32JuA9FD_HCiOx8OA7vXFV9fEk5HcMHuY4rr0tUew11fUGaqUcqA4IjASgd4GTKhI1TkiY9ronPchMQGYtS9IU66/s200/dissociation.png" width="200" /></a><br />
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncRX3RtWUlVbzhuVzg">dissociation original </a> <a href="https://drive.google.com/open?id=0B7QYEhcLQncRUXZhVUhfc3E4SXM"> dissocation converted</a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpfBhuX8noVB3jNr3hvknSDBpQgvYSAtooYlXNBZD7Icep7uMtOpENsZXz-9xxFr_umyEBr3kvshehcoJ6AXZkqsaeTcs7740ktFS5AH9TVzRuR75d-pp5bIPPQ8TWe5U_46ez-77ep2HX/s1600/truncation_CD.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpfBhuX8noVB3jNr3hvknSDBpQgvYSAtooYlXNBZD7Icep7uMtOpENsZXz-9xxFr_umyEBr3kvshehcoJ6AXZkqsaeTcs7740ktFS5AH9TVzRuR75d-pp5bIPPQ8TWe5U_46ez-77ep2HX/s200/truncation_CD.png" width="200" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpfBhuX8noVB3jNr3hvknSDBpQgvYSAtooYlXNBZD7Icep7uMtOpENsZXz-9xxFr_umyEBr3kvshehcoJ6AXZkqsaeTcs7740ktFS5AH9TVzRuR75d-pp5bIPPQ8TWe5U_46ez-77ep2HX/s1600/truncation_CD.png" imageanchor="1"></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW03RvA1RdHnK7-lpJNXeBV34JmfJd9Fwz49mko7CeKl0vwitRvJ6eE2Szuu7KnF3kkhe4PTPFBh_dnylwRVYJZmS5ofHPFUW7MaVrOMC1-YICJ90U1TSd4cYrLyzHFatgCbGRHLbeNWWI/s1600/truncation.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW03RvA1RdHnK7-lpJNXeBV34JmfJd9Fwz49mko7CeKl0vwitRvJ6eE2Szuu7KnF3kkhe4PTPFBh_dnylwRVYJZmS5ofHPFUW7MaVrOMC1-YICJ90U1TSd4cYrLyzHFatgCbGRHLbeNWWI/s200/truncation.png" width="200" /></a></div>
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<a href="https://drive.google.com/open?id=0B7QYEhcLQncRTWk1S3ppVVRiV0k">truncation original </a> <a href="https://drive.google.com/open?id=0B7QYEhcLQncRUWMzNGVQek8xbjA">truncation converted</a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYYX9z6xIjay7c6HFtmb43Yimb0JTwFSbP_DqCZusimahXe23lbmkXWzYnPGbhy45oQzoSzNUW28O_Jo1fYyaaWMlujL_kCLrWH8STwjw-1BogTPL4gf7MSgPst-HVAmXjLGIMBpMV3_97/s1600/ex2.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYYX9z6xIjay7c6HFtmb43Yimb0JTwFSbP_DqCZusimahXe23lbmkXWzYnPGbhy45oQzoSzNUW28O_Jo1fYyaaWMlujL_kCLrWH8STwjw-1BogTPL4gf7MSgPst-HVAmXjLGIMBpMV3_97/s200/ex2.png" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPC_OjlvJEww45BK6INXVCOSw7g2X3WWQG6RR-Dg4BkcET_OaAZjyVx7zMmEWRYYMkXIREmRjhtmh-HgudYuE4wvJ108209idFSq72k2SQK5QfOrsgMfgxPYdbpZu8sUGT5entQqc40Eg3/s1600/layout.png" imageanchor="1"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPC_OjlvJEww45BK6INXVCOSw7g2X3WWQG6RR-Dg4BkcET_OaAZjyVx7zMmEWRYYMkXIREmRjhtmh-HgudYuE4wvJ108209idFSq72k2SQK5QfOrsgMfgxPYdbpZu8sUGT5entQqc40Eg3/s200/layout.png" width="200" /></a></div>
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<div style="text-align: center;">
<a href="https://drive.google.com/open?id=0B7QYEhcLQncRbk5nZmNlc00zOUk">combined original</a> <a href="https://drive.google.com/open?id=0B7QYEhcLQncRWURpRWw0UV9FLWM">combined converted</a></div>
</div>
<div>
<br /></div>
<div>
For next week, I will be working on reactions with bending lines, reactions with modifiers, bezier lines and complexes. And I am hoping to complete the conversion from CellDesigner annotation to SBML Layout before the midterm evaluation.</div>
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Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-46103082957282252612016-05-31T05:36:00.000-07:002016-06-01T08:55:06.772-07:00CellDesigner → SBMLHello all,<br />
<br />
Last week, I have created APIs from schemas. Using the APIs, I have tested if I can get the attributes from XML. With the test, I have figured out that I could not obtain the celldesigner:reactionType attributes (already fixed). <br />
<br />
For the past week, I have been implementing the converter that converts CellDesigner annotation to SBML Layout. The brief outline of the converter is as follow.<br />
<br />
<br />
<ol>
<li>Read XML using the generated APIs</li>
<li>Read XML using JSBML</li>
<li>Copy datas from 1. to the wrappers which were implemented last week</li>
<li>From 3. copy the necessary datas into 2. </li>
</ol>
<div>
So far, I have implemented conversion of compartment and speciesAlias. Figures shown below are the original model created with CellDesigner and the output model visualized with <a href="http://sysbioapps.dyndns.org/Layout">SBML Layout Viewer</a>. As you can see, most diagrams are in the same layout. However the text for each diagram still needs some adjustments. </div>
<div>
<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjX9CSc-W_hi8E17dVBYNfrayHXcZ3Ekrc3z476Dx0gF1W2jg4aizl20ORXNOUwEdHRfeWltKTaa1LgWSf70ebzY2lNzMgfWUr5NCxRunRtOeZBw6L5ZzaZpGROeRFSBYALq-kBl5Ia6ooP/s1600/ex3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjX9CSc-W_hi8E17dVBYNfrayHXcZ3Ekrc3z476Dx0gF1W2jg4aizl20ORXNOUwEdHRfeWltKTaa1LgWSf70ebzY2lNzMgfWUr5NCxRunRtOeZBw6L5ZzaZpGROeRFSBYALq-kBl5Ia6ooP/s320/ex3.jpg" width="320" /></a></div>
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<a href="https://drive.google.com/file/d/0B7QYEhcLQncRY2paN2NvOEpuNjA/view?usp=sharing">Original Model </a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihST8MuAN55e6tbpFJnz1uLxTK_iHGWsrN2WqoNEmgU2x96Hr4PeMXUc5ywSC7U2THzpJiJL5GbdbUhsTOuZHO4ubNe-VAmspq92ysWoZkPpQ8tB2GXoRSeCLwO2rlsQZ3yYDSecs5zzXx/s1600/layout+%25282%2529.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihST8MuAN55e6tbpFJnz1uLxTK_iHGWsrN2WqoNEmgU2x96Hr4PeMXUc5ywSC7U2THzpJiJL5GbdbUhsTOuZHO4ubNe-VAmspq92ysWoZkPpQ8tB2GXoRSeCLwO2rlsQZ3yYDSecs5zzXx/s320/layout+%25282%2529.png" width="320" /></a></div>
<div style="text-align: center;">
<a href="https://drive.google.com/file/d/0B7QYEhcLQncRQXVJTUdsTlBmUUk/view?usp=sharing">Output Model </a></div>
<div style="text-align: center;">
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<div style="text-align: center;">
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<div style="text-align: left;">
For next week, I will be implementing the conversion of reactions (the lines show in the diagram). And I am hoping to start the conversion from SBML layout to CellDesigner.<br />
<br />
<br />
<a href="https://www.blogger.com/"></a><span id="goog_1323777075"></span><span id="goog_1323777076"></span><br /></div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-1029126190506135382016-05-24T22:28:00.002-07:002016-05-24T22:28:31.747-07:00Coding Period beginsHello everyone,<br />
<br />
This week has been the most productive so far and I was able to start coding on schedule.<br />
<br />
<br />
Last week, I had some trouble generating APIs from 3 schemas (CellDesigner.xsd, sbml-level2-v4.xsd, and sbmlCellDesignerExtension_v4_2.xsd) with JAXB. By removing the annotation definition in sbml-level2-v4.xsd and changing the element in CellDesigner.xsd, my mentor and I have succeeded generating the APIs from schemas. It still needs testing but I was able to obtain the CellDesigner extension from species. Below are all the classes that have been generated.<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZcteLgB9QXAHVDYV-nVLz8JSl1DO5_SGSfuuyL4aBSdOdNbEBPgFSc7wMYt1SKlpbwuzabJVFlsDeZgERRKVeXPstW4EMsv4D2C3McroqwxfURIPgXJEu3mI7hKLvITR-5L0gNI4WBv6w/s1600/CellDesigner4ExtensionTagSpecificationE.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="313" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZcteLgB9QXAHVDYV-nVLz8JSl1DO5_SGSfuuyL4aBSdOdNbEBPgFSc7wMYt1SKlpbwuzabJVFlsDeZgERRKVeXPstW4EMsv4D2C3McroqwxfURIPgXJEu3mI7hKLvITR-5L0gNI4WBv6w/s400/CellDesigner4ExtensionTagSpecificationE.jpg" width="400" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeun8KXBiPuHgdjYDOBPy4-8zBmAwxaCtMKY_l5BjuxDfb5uPZGru3IeJsXVYGjObYO0eZat_wfda-95df2UYWhVAmzEFBXJbRo_Frpdn7e2WtnudiIHg5v2783AHD6OXTzyr_hv5nKXg3/s1600/celld.001-1.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeun8KXBiPuHgdjYDOBPy4-8zBmAwxaCtMKY_l5BjuxDfb5uPZGru3IeJsXVYGjObYO0eZat_wfda-95df2UYWhVAmzEFBXJbRo_Frpdn7e2WtnudiIHg5v2783AHD6OXTzyr_hv5nKXg3/s320/celld.001-1.jpg" style="cursor: move;" width="191" /></a></div>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeun8KXBiPuHgdjYDOBPy4-8zBmAwxaCtMKY_l5BjuxDfb5uPZGru3IeJsXVYGjObYO0eZat_wfda-95df2UYWhVAmzEFBXJbRo_Frpdn7e2WtnudiIHg5v2783AHD6OXTzyr_hv5nKXg3/s1600/celld.001-1.jpg" imageanchor="1"></a><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2sl7UwEq-WbpcqyVX3Q7hXVRGSJVf7XGGB25NJZZv2odGg_8Dk5EKeENGQ_Ts6Th_XJULEY0EcBXPChK8H2BmGWlADf5y2IiXZi9pLCa79Ul3aTKMDEvM1mu_4FkW4CjN1SZ2PfhVQwPy/s320/celld.001-0.jpg" width="130" /><br />
<br />
<br />
For the generated APIs, I have been creating some utility classes for easier use. Since CellDesigner annotates model, compartment, species, reaction, speciesReference, and modifiedSpeciesReference, I have created wrapper classes to easily access the extended attributes for all of them. And also for speciesAlias.<br />
<br />
For next week, I will do mainly two things. First is to test the generated APIs for the CellDesigner extended attributes. Second thing is to create classes that clones from unmarshalled data structure to the wrapper classes. Once I have checked that all datas are stored properly, I will start implementing the actual converter.<br />
<br />
<br />
<br />
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-64266016666306834732016-05-19T04:22:00.003-07:002016-05-19T04:22:57.410-07:00Meeting May 18Hello all,<div>
<br /></div>
<div>
As I have mentioned in the previous blog post, my mentors and I needed to figure out a way to create a API for CellDesigner annotation using 3 schema files (CellDesigner.xsd, sbmlCellDesignerExtension_v2_5.xsd, and sbml-level-2-v1.xsd). In yesterday's meeting, we have come up with 3 ideas.</div>
<div>
<br /></div>
<div>
<ul>
<li>remove the definition of annotation in the sbml-level-2-v1.xsd to remove the conflicts with other schema. (Thanks to Dr. Keating and Dr. Bergmann)</li>
<li>create a schema file from CellDesigner classes</li>
<li>use CellDesignerAnnotationParser which manually parses CellDesigner annotation</li>
</ul>
</div>
<div>
For this week, I will be working on the first plan and leave the two other options as a backup plan. I will start by familiarizing myself to XML schema and hopefully solve this schema problem by next week.</div>
Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-63698537666754017922016-05-17T20:32:00.000-07:002016-05-17T22:08:22.589-07:00Week 3Hello everyone,<br />
<br />
sorry for not posting last week. I have been a bit busy with other stuff.<br />
<br />
So far I have done the following.<br />
<ul>
<li>Downloaded JSBML maven project </li>
<li>Created sample program to try out the API for the layout</li>
<li>Read GSoC 2014 project code by Ibrahim Vazirabad <span style="background-color: white; color: #333333; font-family: "arial" , "tahoma" , "helvetica" , "freesans" , sans-serif; font-size: 14.85px; line-height: 20.79px;">and his <a href="http://jsbmlcelldesigner2014.blogspot.jp/">blog</a></span></li>
</ul>
<div>
<br />
As the first step of my project, I must figure out a way to create an API for CellDesigner annotation in a SBML file. Since it will be a standalone software, the software can not use the CellDesigner as Ibrahim did. After this has been resolved, I will be working on to convert the CellDesigner annotation to pure SBML with layout extension.<br />
<br />
<br />
In Ibrahim's project, he mentioned how CellDesigner classes are mapped to that of SBML. I thought it will be useful so I will post it here for future reference.<br />
<br />
<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4Tf_7JCa47p5NEt4HiPUbjAC2cLXPJjBB8nnft8cGFpAH6g1KrjmGa2KsH4L4TbUb6t54GCOAxkrb0tW9fcTj_5EWMpFmttgUp5WeyQyTNoSHMuOfsWqMDM4OtxMUFcavhWa59j0O8iBc/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4Tf_7JCa47p5NEt4HiPUbjAC2cLXPJjBB8nnft8cGFpAH6g1KrjmGa2KsH4L4TbUb6t54GCOAxkrb0tW9fcTj_5EWMpFmttgUp5WeyQyTNoSHMuOfsWqMDM4OtxMUFcavhWa59j0O8iBc/s320/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" width="320" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_4ANWlbFv8xBdfiGZCuVUEUHEc0QTvZqeQg1yJvLNj9J9cB2Vordens2X9YBMy7VJXuT__KKJCREHpv0rka6aT5j8WOjIJPiJuLpY0Pb7ED5ZPNdnX8QDihjDwRGKtWmg0i4YWab68_Zw/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-8-638.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_4ANWlbFv8xBdfiGZCuVUEUHEc0QTvZqeQg1yJvLNj9J9cB2Vordens2X9YBMy7VJXuT__KKJCREHpv0rka6aT5j8WOjIJPiJuLpY0Pb7ED5ZPNdnX8QDihjDwRGKtWmg0i4YWab68_Zw/s320/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-8-638.jpg" width="320" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIk84HAt-rsKyGVXw5EvubVckaKPPfu-qTbIKLzQGZOVseNOOOgv5QSenEP2Mka5r-BKGewcaoDXfGp_NFd5IYmnqJiChDnvJARI9iRGfS0BQTeXUm4R1CTxQbVe-vzRIzrCduEAPaNVSh/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-9-638.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIk84HAt-rsKyGVXw5EvubVckaKPPfu-qTbIKLzQGZOVseNOOOgv5QSenEP2Mka5r-BKGewcaoDXfGp_NFd5IYmnqJiChDnvJARI9iRGfS0BQTeXUm4R1CTxQbVe-vzRIzrCduEAPaNVSh/s320/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-9-638.jpg" width="320" /></a></div>
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<br />
Also to check if my conversion is correct, the <a href="http://sysbioapps.dyndns.org/Layout">SBML Layout Viewer</a> by Dr. Frank Bergmann may be come in handy.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_WHYYureYIY5EcK6L5zD5awp12v8tKdNjkJWGUQpHeSdXmLiFeLiZPKTsJji3Z-0w2kx5X1oJI-XSPruk_4xecZ5DaPReI2qzXLoZnNZLVjKRSPIVPIMEjvJrW0T7IH3WVvzgGEozMihU/s1600/improving-the-jsbmlcelldesigner-plugin-interface-combine-2014-10-638.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a>Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com0tag:blogger.com,1999:blog-7053847733245746410.post-41006332551348297942016-04-27T05:26:00.001-07:002016-04-27T05:26:08.323-07:00IntroHello all!<br />
<br />
My name is Kaito Ii. I am grad student working on my Master's degree at <a href="http://fun.bio.keio.ac.jp/">Funahashi Lab.</a> This summer, I will be participating in GSoC 2016 (Google Summer of Code). As my project, I will be implementing a standalone software that converts <a href="http://www.celldesigner.org/">CellDesigner</a> annotation to <a href="http://sbml.org/Main_Page">SBML</a> Layout extension and vice versa. This will allow to have the same visual layout of a model between CellDesigner and other softwares.<br />
<br />
I am looking forward to working on this project. I am sure that it will be a great summer.Anonymoushttp://www.blogger.com/profile/13623129285695363226noreply@blogger.com03 Chome-14 Hiyoshi, Kōhoku-ku, Yokohama-shi, Kanagawa-ken 223-0061, Japan35.555552084426651 139.6540403366088935.55393708442665 139.65151883660889 35.557167084426652 139.65656183660889