http://2009.igem.org/wiki/index.php?title=Special:Contributions/Jlapointe&feed=atom&limit=50&target=Jlapointe&year=&month=2009.igem.org - User contributions [en]2023-12-03T01:05:51ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:Waterloo/NotebookTeam:Waterloo/Notebook2009-10-21T18:46:30Z<p>Jlapointe: /* Safety */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
==Oligos==<br />
A list of all [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes.<br />
<br />
==Strain List==<br />
The strain list that we used to manage our freezer stocks.<br />
<br />
==Safety==<br />
<br />
Health risks to lab researchers are minimal because the organisms used are all Biosafety level 1--our project does not involve any genes from human pathogens or plant pathogens. <br />
<br />
All precautions with respect to recombinant DNA are observed:<br />
<br />
*All waste is autoclaved before being thrown away.<br />
*Researchers practice aseptic technique, and frequent hand washing.<br />
*Bench surfaces are disinfected with ethanol</div>Jlapointehttp://2009.igem.org/Team:Waterloo/TeamTeam:Waterloo/Team2009-10-21T18:45:56Z<p>Jlapointe: /* Who we are */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
== <br><Br>'''Who we are''' ==<br />
<br />
<table border="0"><br />
<tr><td colspan=2>The University of Waterloo's 2009 iGEM Team is a dynamic group, consisting of students from the Faculties of Science, Engineering, and Mathematics. We are an undergraduate-run team, with a student Director managing most of our team's affairs and directing our team's ongoing activities. Our enthusiastic Faculty Instructors and Advisors give us the benefit of their experience and, in the case of Dr. Trevor Charles, lab space, and provide us with additional support and guidance in areas related to design, mathematical modeling, lab work and administration. </td><br />
</tr><br />
<tr><br />
<td align="left"> <br />
<br />
<br />
Because of Waterloo's co-op program, some of our members take courses during the summer, while others work full-time. The majority of our team members participate in the iGEM competition in their spare time, outside of work or school; a few have been involved part-time as part of their research-assistant positions in various labs in the UW Department of Biology. This team structure means that instead of each member taking on one aspect of the project to tackle over the course of the summer, our team collectively works on the project as a whole, each member picking up where the last left off the day before, or even earlier the same day!<br />
<br />
UW iGEM Team members are all involved in a unique learning experience: our 2009 team consists largely of students who started with little or no research/laboratory experience and had a range of theoretical knowledge of molecular biology. With a desire to learn and guidance from more experienced teammates, these students have become comfortable working in a lab environment, and our senior members have had valuable opportunities to share their experience with others.<br />
</table><br />
<br><br><br />
<br />
==<b> Undergraduate Students</b>==<br />
<br />
<table border="0"><br />
<tr><br />
<br />
<td align="left"> [[Image:WikiJH.JPG|center]] </td><br />
<td align="center"> <b> John Heil</b> </td><br />
<td align="left" > Lab and Design Team Leader, <br> Biology</td><br />
<br />
</tr><br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Patrick_MacKinnon.PNG|center]] </td><br />
<td align="center"> <b> Patrick MacKinnon </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Chemical Engineering</td><br />
<br />
</tr><br />
<tr><br />
<br />
<td align="left"> [[Image:Harsh_Parikh.JPG|center]] </td><br />
<td align="center"> <b> Harsh Parikh </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Biology </td><br />
<br />
</tr><br />
<tr><br />
<td align="left"> [[Image:WyleeCo.jpg|center]]</td><br />
<td align="center"> <b> Wylee Co </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Nanotechnology Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Nasra_Aidarus.jpg|center]]</td><br />
<td align="center"> <b> Nasra Aidarus </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr> <br />
<td align="left"> [[Image:Tim Picture2.jpg|center]]</td><br />
<td align="center"> <b> Tim Lin </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Sandy_Mclachlang.png|center|150x150px]] </td><br />
<td align="center"> <b> Sandy Mclachlan </b> </td><br />
<td align="left" > Lab Team Member <br> Biology </td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left"> [[Image:Leah_Kocsis.jpg|center]] </td><br />
<td align="center"> <b> Leah Kocsis </b> </td><br />
<td align="left" > Human Practices/Outreach Leader <br> Science & Business</td><br />
</tr><br />
<tr><br />
<td align="left"> [[Image:Brandon_Wang.png|center|150x150px]] </td><br />
<td align="center"> <b> Brandon Wang </b> </td><br />
<td align="left" > Modeling Team Member <br> Electrical Engineering</td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left"> [[Image:Matthew_Gingerich.png|center|150x150px]] </td><br />
<td align="center"> <b> Matthew Gingerich </b> </td><br />
<td align="left" > Modeling Team Member <br> Systems Design Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Jordan_Lapointe.jpg|center|150x150px]] </td><br />
<td align="center"> <b> Jordan Lapointe </b> </td><br />
<td align="left" > Modeling Team Member <br> Mathematical Physics</td><br />
</tr><br />
<tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Hillary_Yeung.png|center|150x150px]] </td><br />
<td align="center"> <b> Hillary Yeung </b> </td><br />
<td align="left" > Assistant to the Director <br> Chemical Engineering</td><br />
</tr><br />
<br />
<br />
</table><br />
<br />
==<b>Graduate Students</b>==<br />
<table border="0"><br />
<br />
<tr><br />
<td align="left"> [[Image:Andre_Masella.png|center]] </td><br />
<td align="center"> <b> Andre Masella </b> </td><br />
<td align="left" > Team Jack-of-all-trades, Modeling Subteam Lead <br> Computer Engineering</td><br />
</tr> <br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Eddie_Ma.PNG|center]] </td><br />
<td align="center"> <b> Eddie Yee Tak Ma </b> </td><br />
<td align="left" > Modeling Subteam Associate Lead <br> Bioinformatics, Biochemistry</td><br />
<br />
</tr><br />
</table><br />
<br />
==<b>Faculty Instructors</b>==<br />
<table><br />
<tr><br />
<td align="left">[[Image:Brian_Ingalls.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Brian Ingalls </b><br><br />
Team Founder/Mathematical Modelling Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Trevor_Charles.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Trevor Charles</b><br><br />
Lab Advisor, Provider of All-Important Lab Space<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Barb_Moffatt.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Barb Moffatt </b><br><br />
Administration/Fundraising Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Marc_Aucoin.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Marc Aucoin </b><br><br />
Co-op Supervisor<br><br />
</td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left">[[Image:Josh_Neufeld.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Josh Neufeld </b><br><br />
Co-op Supervisor<br><br />
</td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left">[[Image:Matt_Scott.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Matthew Scott </b><br><br />
Co-op Supervisor<br><br />
</td><br />
</tr><br />
<br />
<br />
</table><br />
<br><br><br />
<br />
==Sponsors==<br />
Supported by:<br />
<br />
[[Image:UWiGEMSciFac.png|center]]<br />
<br />
[[Image:UWiGEMBioDept.png|center]]<br />
<br />
[[Image:UWiGEMWatSef.png|center]]<br />
<br />
[[Image:UWiGEMNSERC.png|center]]<br />
<br />
[[Image:UWiGEMMEF.png|center]]<br />
<br />
[[Image:UWiGEMWEEF.png|center]]<br />
<br />
[[Image:UWiGEMNEB.png|center]]<br />
<br />
[[Image:UWiGEMFermentas.png|center]]</div>Jlapointehttp://2009.igem.org/Team:Waterloo/NotebookTeam:Waterloo/Notebook2009-10-21T18:42:54Z<p>Jlapointe: /* Safety */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
==Oligos==<br />
A list of all [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes.<br />
<br />
==Strain List==<br />
The strain list that we used to manage our freezer stocks.<br />
<br />
==Safety==<br />
<br />
Health risks to lab researchers working on the project are minimal because the organisms used are all Biosafety level 1--our project does not involve any genes from human pathogens or plant pathogens. <br />
<br />
All precautions with respect to recombinant DNA are observed:<br />
<br />
*All waste is autoclaved before being thrown away.<br />
*Researchers practice aseptic technique, and frequent hand washing.<br />
*Bench surfaces are disinfected with ethanol</div>Jlapointehttp://2009.igem.org/Team:Waterloo/NotebookTeam:Waterloo/Notebook2009-10-21T18:41:17Z<p>Jlapointe: /* Safety */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
==Oligos==<br />
A list of all [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes.<br />
<br />
==Strain List==<br />
The strain list that we used to manage our freezer stocks.<br />
<br />
==Safety==<br />
<br />
Our project does not involve any genes from human pathogens or plant pathogens. Health risks to lab researchers working on the project are minimal because the organisms used are all Biosafety level 1. <br />
<br />
All precautions with respect to recombinant DNA are observed:<br />
<br />
*All waste is autoclaved before being thrown away.<br />
*Researchers practice aseptic technique, and frequent hand washing.<br />
*Bench surfaces are disinfected with ethanol</div>Jlapointehttp://2009.igem.org/Team:Waterloo/NotebookTeam:Waterloo/Notebook2009-10-21T18:39:18Z<p>Jlapointe: /* Safety */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
==Oligos==<br />
A list of all [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes.<br />
<br />
==Strain List==<br />
The strain list that we used to manage our freezer stocks.<br />
<br />
==Safety==<br />
<br />
Our project does not involve any genes from human pathogens or plant pathogens. The risk to researchers involved with the project is minimal because the organisms used are all Biosafety level 1. <br />
<br />
All precautions with respect to recombinant DNA are observed:<br />
<br />
*All waste is autoclaved before being thrown away.<br />
*Researchers practice aseptic technique, and frequent hand washing.<br />
*Bench surfaces are disinfected with ethanol</div>Jlapointehttp://2009.igem.org/Team:Waterloo/NotebookTeam:Waterloo/Notebook2009-10-21T18:36:48Z<p>Jlapointe: /* Safety */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
==Oligos==<br />
A list of all [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes.<br />
<br />
==Strain List==<br />
The strain list that we used to manage our freezer stocks.<br />
<br />
==Safety==<br />
<br />
Our project does not involve any genes from human pathogens or plant pathogens. Risk to researchers is minimal because the organisms used are all Biosafety level 1. <br />
<br />
All precautions with respect to recombinant DNA have been taken. <br />
<br />
*All waste is autoclaved before being thrown away.<br />
*Researchers practice aseptic technique, and frequent hand washing.<br />
*Bench surfaces are disinfected with ethanol</div>Jlapointehttp://2009.igem.org/Team:Waterloo/TeamTeam:Waterloo/Team2009-10-20T22:32:15Z<p>Jlapointe: /* Undergraduate Students */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
== <br><Br>'''Who we are''' ==<br />
<br />
<table border="0"><br />
<tr><td colspan=2>The University of Waterloo's 2009 iGEM Team is a dynamic group, consisting of students from the Faculties of Science, Engineering, and Mathematics. We are an undergraduate-run team, with a student Director managing most of our team's affairs and directing our team's ongoing activities. Our enthusiastic Faculty Instructors and Advisors give us the benefit of their experience and, in the case of Dr. Trevor Charles, lab space, and provide us with additional support and guidance in areas related to design, mathematical modelling, lab work and administration. </td><br />
</tr><br />
<tr><br />
<td align="left"> <br />
<br />
<br />
Because of Waterloo's co-op program, some of our members take courses during the summer, while others work full-time. The majority of our team members participate in the iGEM competition in their spare time, outside of work or school; a few have been involved part-time as part of their research-assistant positions in various labs in the UW Department of Biology. This team structure means that instead of each member taking on one aspect of the project to tackle over the course of the summer, our team collectively works on the project as a whole, each member picking up where the last left off the day before, or even earlier the same day!<br />
<br />
UW iGEM Team members are all involved in a unique learning experience: our 2009 team consists largely of students who started with little or no research/laboratory experience and had a range of theoretical knowledge of molecular biology. With a desire to learn and guidance from more experienced teammates, these students have become comfortable working in a lab environment, and our senior members have had valuable opportunities to share their experience with others.<br />
</table><br />
<br><br><br />
<br />
==<b> Undergraduate Students</b>==<br />
<br />
<table border="0"><br />
<tr><br />
<br />
<td align="left"> [[Image:WikiJH.JPG|center]] </td><br />
<td align="center"> <b> John Heil</b> </td><br />
<td align="left" > Lab and Design Team Leader, <br> Biology</td><br />
<br />
</tr><br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Patrick_MacKinnon.PNG|center]] </td><br />
<td align="center"> <b> Patrick MacKinnon </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Chemical Engineering</td><br />
<br />
</tr><br />
<tr><br />
<br />
<td align="left"> [[Image:Harsh_Parikh.JPG|center]] </td><br />
<td align="center"> <b> Harsh Parikh </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Biology </td><br />
<br />
</tr><br />
<tr><br />
<td align="left"> [[Image:WyleeCo.jpg|center]]</td><br />
<td align="center"> <b> Wylee Co </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Nanotechnology Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Nasra_Aidarus.jpg|center]]</td><br />
<td align="center"> <b> Nasra Aidarus </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr> <br />
<td align="left"> [[Image:Tim Picture2.jpg|center]]</td><br />
<td align="center"> <b> Tim Lin </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Sandy_Mclachlang.png|center|150x150px]] </td><br />
<td align="center"> <b> Sandy Mclachlan </b> </td><br />
<td align="left" > Lab Team Member <br> Biology </td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left"> [[Image:Leah_Kocsis.jpg|center]] </td><br />
<td align="center"> <b> Leah Kocsis </b> </td><br />
<td align="left" > Human Practices/Outreach Leader <br> Science & Business</td><br />
</tr><br />
<tr><br />
<td align="left"> [[Image:Brandon_Wang.png|center|150x150px]] </td><br />
<td align="center"> <b> Brandon Wang </b> </td><br />
<td align="left" > Modeling Team Member <br> Electrical Engineering</td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left"> [[Image:Matthew_Gingerich.png|center|150x150px]] </td><br />
<td align="center"> <b> Matthew Gingerich </b> </td><br />
<td align="left" > Modeling Team Member <br> Systems Design Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Jordan_Lapointe.jpg|center|150x150px]] </td><br />
<td align="center"> <b> Jordan Lapointe </b> </td><br />
<td align="left" > Modeling Team Member <br> Mathematical Physics</td><br />
</tr><br />
<tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Hillary_Yeung.png|center|150x150px]] </td><br />
<td align="center"> <b> Hillary Yeung </b> </td><br />
<td align="left" > Assistant to the Director <br> Chemical Engineering</td><br />
</tr><br />
<br />
<br />
</table><br />
<br />
==<b>Graduate Students</b>==<br />
<table border="0"><br />
<br />
<tr><br />
<td align="left"> [[Image:Andre_Masella.png|center]] </td><br />
<td align="center"> <b> Andre Masella </b> </td><br />
<td align="left" > Team Jack-of-all-trades, Modeling Subteam Lead <br> Computer Engineering</td><br />
</tr> <br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Eddie_Ma.PNG|center]] </td><br />
<td align="center"> <b> Eddie Yee Tak Ma </b> </td><br />
<td align="left" > Modeling Subteam Associate Lead <br> Bioinformatics, Biochemistry</td><br />
<br />
</tr><br />
</table><br />
<br />
==<b>Faculty Instructors</b>==<br />
<table><br />
<tr><br />
<td align="left">[[Image:Brian_Ingalls.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Brian Ingalls </b><br><br />
Team Founder/Mathematical Modelling Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Trevor_Charles.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Trevor Charles</b><br><br />
Lab Advisor, Provider of All-Important Lab Space<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Barb_Moffatt.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Barb Moffatt </b><br><br />
Administration/Fundraising Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Marc_Aucoin.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Marc Aucoin </b><br><br />
Co-op Supervisor<br><br />
</td><br />
</tr><br />
<br />
<br />
</table><br />
<br><br><br />
<br />
<br />
==Sponsors==<br />
Supported by:<br />
<br />
[[Image:UWiGEMSciFac.png|center]]<br />
<br />
[[Image:UWiGEMBioDept.png|center]]<br />
<br />
[[Image:UWiGEMWatSef.png|center]]<br />
<br />
[[Image:UWiGEMNSERC.png|center]]<br />
<br />
[[Image:UWiGEMMEF.png|center]]<br />
<br />
[[Image:UWiGEMWEEF.png|center]]<br />
<br />
[[Image:UWiGEMNEB.png|center]]<br />
<br />
[[Image:UWiGEMFermentas.png|center]]</div>Jlapointehttp://2009.igem.org/File:Jordan_Lapointe.jpgFile:Jordan Lapointe.jpg2009-10-20T22:29:25Z<p>Jlapointe: </p>
<hr />
<div></div>Jlapointehttp://2009.igem.org/Team:Waterloo/TeamTeam:Waterloo/Team2009-10-20T22:28:29Z<p>Jlapointe: /* Undergraduate Students */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
== <br><Br>'''Who we are''' ==<br />
<br />
<table border="0"><br />
<tr><td colspan=2>The University of Waterloo's 2009 iGEM Team is a dynamic group, consisting of students from the Faculties of Science, Engineering, and Mathematics. We are an undergraduate-run team, with a student Director managing most of our team's affairs and directing our team's ongoing activities. Our enthusiastic Faculty Instructors and Advisors give us the benefit of their experience and, in the case of Dr. Trevor Charles, lab space, and provide us with additional support and guidance in areas related to design, mathematical modelling, lab work and administration. </td><br />
</tr><br />
<tr><br />
<td align="left"> <br />
<br />
<br />
Because of Waterloo's co-op program, some of our members take courses during the summer, while others work full-time. The majority of our team members participate in the iGEM competition in their spare time, outside of work or school; a few have been involved part-time as part of their research-assistant positions in various labs in the UW Department of Biology. This team structure means that instead of each member taking on one aspect of the project to tackle over the course of the summer, our team collectively works on the project as a whole, each member picking up where the last left off the day before, or even earlier the same day!<br />
<br />
UW iGEM Team members are all involved in a unique learning experience: our 2009 team consists largely of students who started with little or no research/laboratory experience and had a range of theoretical knowledge of molecular biology. With a desire to learn and guidance from more experienced teammates, these students have become comfortable working in a lab environment, and our senior members have had valuable opportunities to share their experience with others.<br />
</table><br />
<br><br><br />
<br />
==<b> Undergraduate Students</b>==<br />
<br />
<table border="0"><br />
<tr><br />
<br />
<td align="left"> [[Image:WikiJH.JPG|center]] </td><br />
<td align="center"> <b> John Heil</b> </td><br />
<td align="left" > Lab and Design Team Leader, <br> Biology</td><br />
<br />
</tr><br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Patrick_MacKinnon.PNG|center]] </td><br />
<td align="center"> <b> Patrick MacKinnon </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Chemical Engineering</td><br />
<br />
</tr><br />
<tr><br />
<br />
<td align="left"> [[Image:Harsh_Parikh.JPG|center]] </td><br />
<td align="center"> <b> Harsh Parikh </b> </td><br />
<td align="left" > Lab Team Member, Summer Co-op <br> Biology </td><br />
<br />
</tr><br />
<tr><br />
<td align="left"> [[Image:WyleeCo.jpg|center]]</td><br />
<td align="center"> <b> Wylee Co </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Nanotechnology Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Nasra_Aidarus.jpg|center]]</td><br />
<td align="center"> <b> Nasra Aidarus </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr> <br />
<td align="left"> [[Image:Tim Picture2.jpg|center]]</td><br />
<td align="center"> <b> Tim Lin </b></td><br />
<td align="left"> Lab Team Member, Summer Co-op <br> Biology</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Leah_Kocsis.jpg|center]] </td><br />
<td align="center"> <b> Leah Kocsis </b> </td><br />
<td align="left" > Human Practices/Outreach Leader <br> Science & Business</td><br />
</tr><br />
<tr><br />
<td align="left"> [[Image:Brandon_Wang.png|center|150x150px]] </td><br />
<td align="center"> <b> Brandon Wang </b> </td><br />
<td align="left" > Modeling Team Member <br> Electrical Engineering</td><br />
</tr><br />
<br />
<br />
<tr><br />
<td align="left"> [[Image:Matthew_Gingerich.png|center|150x150px]] </td><br />
<td align="center"> <b> Matthew Gingerich </b> </td><br />
<td align="left" > Modeling Team Member <br> Systems Design Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Jordan_Lapointe.jpg|center|150x150px]] </td><br />
<td align="center"> <b> Jordan Lapointe </b> </td><br />
<td align="left" > Modeling Team Member <br> Mathematical Physics</td><br />
</tr><br />
<tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Hillary_Yeung.png|center|150x150px]] </td><br />
<td align="center"> <b> Hillary Yeung </b> </td><br />
<td align="left" > Assistant to the Director <br> Chemical Engineering</td><br />
</tr><br />
<br />
<tr><br />
<td align="left"> [[Image:Sandy_Mclachlang.png|center|150x150px]] </td><br />
<td align="center"> <b> Sandy Mclachlan </b> </td><br />
<td align="left" > Lab Team Member <br> Biology </td><br />
</tr><br />
<br />
</table><br />
<br />
==<b>Graduate Students</b>==<br />
<table border="0"><br />
<br />
<tr><br />
<td align="left"> [[Image:Andre_Masella.png|center]] </td><br />
<td align="center"> <b> Andre Masella </b> </td><br />
<td align="left" > Team Jack-of-all-trades, Modeling Subteam Lead <br> Computer Engineering</td><br />
</tr> <br />
<br />
<tr><br />
<br />
<td align="left"> [[Image:Eddie_Ma.PNG|center]] </td><br />
<td align="center"> <b> Eddie Yee Tak Ma </b> </td><br />
<td align="left" > Modeling Subteam Associate Lead <br> Bioinformatics, Biochemistry</td><br />
<br />
</tr><br />
</table><br />
<br />
==<b>Faculty Instructors</b>==<br />
<table><br />
<tr><br />
<td align="left">[[Image:Brian_Ingalls.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Brian Ingalls </b><br><br />
Team Founder/Mathematical Modelling Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Trevor_Charles.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Trevor Charles</b><br><br />
Lab Advisor, Provider of All-Important Lab Space<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Barb_Moffatt.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Barb Moffatt </b><br><br />
Administration/Fundraising Advisor<br><br />
</td><br />
</tr><br />
<br />
<tr><br />
<td align="left">[[Image:Marc_Aucoin.PNG|center|150x150px]]</td><br />
<td align="center"> <b> Dr. Marc Aucoin </b><br><br />
Co-op Supervisor<br><br />
</td><br />
</tr><br />
<br />
<br />
</table><br />
<br><br><br />
<br />
<br />
==Sponsors==<br />
Supported by:<br />
<br />
[[Image:UWiGEMSciFac.png|center]]<br />
<br />
[[Image:UWiGEMBioDept.png|center]]<br />
<br />
[[Image:UWiGEMWatSef.png|center]]<br />
<br />
[[Image:UWiGEMNSERC.png|center]]<br />
<br />
[[Image:UWiGEMMEF.png|center]]<br />
<br />
[[Image:UWiGEMWEEF.png|center]]<br />
<br />
[[Image:UWiGEMNEB.png|center]]<br />
<br />
[[Image:UWiGEMFermentas.png|center]]</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T07:19:39Z<p>Jlapointe: /* Software */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we made several assumptions. First, as we did not know which combinations of sequences with ''att'' sites would be part of the solution, we assumed that any product in our search space was a valid sequence for the next generation of reactions. <br />
<br />
We further assumed that any plasmid with valid ''att'' sites and complementary operators was capable of self reacting and also of reacting with any other plasmid in the history of the modeled cell. <br />
<br />
Lastly, because of the exponential behaviour of the search space, we assumed that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption was made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch of investigation arose out of the necessity to tend to the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene of interest flanked by two ''attB'' sites and the chromosome has a marker flanked by two ''attP'' sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to ''attL'', and the marker will be in the plasmid, where the flanking sites will be changed to ''attR''. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members postulated a potentially-viable recursive recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several rounds of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our biological system, the initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a re-implementation in C++ was initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. We hope that the C++ version will significantly reduce our algorithm's running time, but given the combinatorial explosion in the Python version, this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that may have led to our simulation's reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continuing to search non-obvious rigorous methods to determine a steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T07:14:11Z<p>Jlapointe: /* Conclusion */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we make several assumptions. First, as we do not know which combinations of sequences with ''att'' sites are part of the solution, we assume that any product in our search space is a valid sequence for the next generation of reactions. <br />
<br />
We further assume that any plasmid with valid ''att'' sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. <br />
<br />
Lastly, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch of investigation arose out of the necessity to tend to the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene of interest flanked by two ''attB'' sites and the chromosome has a marker flanked by two ''attP'' sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to ''attL'', and the marker will be in the plasmid, where the flanking sites will be changed to ''attR''. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members postulated a potentially-viable recursive recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several rounds of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our biological system, the initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a re-implementation in C++ was initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. We hope that the C++ version will significantly reduce our algorithm's running time, but given the combinatorial explosion in the Python version, this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that may have led to our simulation's reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continuing to search non-obvious rigorous methods to determine a steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T07:08:11Z<p>Jlapointe: /* Results */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we make several assumptions. First, as we do not know which combinations of sequences with ''att'' sites are part of the solution, we assume that any product in our search space is a valid sequence for the next generation of reactions. <br />
<br />
We further assume that any plasmid with valid ''att'' sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. <br />
<br />
Lastly, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch of investigation arose out of the necessity to tend to the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene of interest flanked by two ''attB'' sites and the chromosome has a marker flanked by two ''attP'' sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to ''attL'', and the marker will be in the plasmid, where the flanking sites will be changed to ''attR''. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members postulated a potentially-viable recursive recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several rounds of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our given biological system, our initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a C++ port had been initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. Given the combinatorial explosion in the Python version, we hope that the C++ version will have better memory efficiency, but this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that the team could have taken that may have lead to our simulations reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek to solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continue searching non-obvious rigorous methods to compute a biological systems steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T07:03:59Z<p>Jlapointe: /* Math */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we make several assumptions. First, as we do not know which combinations of sequences with ''att'' sites are part of the solution, we assume that any product in our search space is a valid sequence for the next generation of reactions. <br />
<br />
We further assume that any plasmid with valid ''att'' sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. <br />
<br />
Lastly, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch of investigation arose out of the necessity to tend to the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene on interest flanked by two attB sites and the chromosome has a marker flanked by two attP sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to attL, and the marker will be in the plasmid, where the flanking sites will be changed to attR. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members designed a theoretical stackable recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several round of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our given biological system, our initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a C++ port had been initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. Given the combinatorial explosion in the Python version, we hope that the C++ version will have better memory efficiency, but this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that the team could have taken that may have lead to our simulations reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek to solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continue searching non-obvious rigorous methods to compute a biological systems steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T06:59:08Z<p>Jlapointe: /* Software */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we make several assumptions. First, as we do not know which combinations of sequences with ''att'' sites are part of the solution, we assume that any product in our search space is a valid sequence for the next generation of reactions. <br />
<br />
We further assume that any plasmid with valid ''att'' sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. <br />
<br />
Lastly, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch morphed out of the necessity to tend the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene on interest flanked by two attB sites and the chromosome has a marker flanked by two attP sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to attL, and the marker will be in the plasmid, where the flanking sites will be changed to attR. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members designed a theoretical stackable recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several round of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our given biological system, our initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a C++ port had been initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. Given the combinatorial explosion in the Python version, we hope that the C++ version will have better memory efficiency, but this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that the team could have taken that may have lead to our simulations reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek to solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continue searching non-obvious rigorous methods to compute a biological systems steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T06:53:40Z<p>Jlapointe: /* Introduction */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome an arbitrary number of desired sequences.<br />
<br />
The form that the solution could take, we postulated, would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modeling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver, however, revealed that the problem is NP-hard at least, and NP-complete at worst. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we had to make a few assumptions. First, as we do not know what combination of sequences with att sites is part of the solution, we assume that any product in our search space is fair game for the next generation of reactions. We further assume that any plasmid with valid att sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. Second, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This second assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch morphed out of the necessity to tend the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene on interest flanked by two attB sites and the chromosome has a marker flanked by two attP sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to attL, and the marker will be in the plasmid, where the flanking sites will be changed to attR. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members designed a theoretical stackable recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several round of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our given biological system, our initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a C++ port had been initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. Given the combinatorial explosion in the Python version, we hope that the C++ version will have better memory efficiency, but this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that the team could have taken that may have lead to our simulations reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek to solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continue searching non-obvious rigorous methods to compute a biological systems steady state.</div>Jlapointehttp://2009.igem.org/Team:Waterloo/ModelingTeam:Waterloo/Modeling2009-10-19T06:49:34Z<p>Jlapointe: /* Abstract */</p>
<hr />
<div>{{Team:Waterloo/NavBar}}<br />
<br />
===Abstract===<br />
<br />
The primary goal of our software was to model integrase mediated DNA rearrangement. After our software was capable of simulating a biological system to steady state, our secondary goal was to be able to generate the initial reactants needed to arrive at a given end state. It was found that our brute force approach could not be used to achieve the second goal as the simulation would run out of hardware resources.<br />
<br />
===Introduction===<br />
<br />
The mathematical modeling component of this year's project consisted of a computational simulation of DNA recombination as mediated by the ΦC31 integrase enzyme. The necessity for this simulation arose directly from challenges faced by the design team in its attempts to create a recursively repeatable technique for inserting sequences of interest onto chromosomes. Specifically, it was noted that manually examining the possible results of interactions between DNA strands quickly becomes infeasible due to the number of potential reaction pathways.<br />
<br />
The first stage of the modeling project was therefore to formally codify the reaction rules employed by the design team with the aim of applying computational power to the problem. The predominant challenge faced at this stage was to abstract the concept of DNA strands into a computationally workable form along with developing mathematically rigorous definitions of the behaviours of reaction sites.<br />
<br />
Formally, the grand object of the modeling project was the determination of a finite deterministic sequence of ''att'' sites and their enclosed operators that would allow one to predictably insert into a chromosome all of the desired sequences.<br />
<br />
The form that the solution could take, we postulated would be a sequence of two or three plasmids such that each would contain at least one matching set of ''att'' sites with the addition of several incomplete ''att'' sites.<br />
<br />
There were two general approaches used in modelling. Software development toward a top-down (inductive, brute force) solver has finished. Characterization of the algorithm underpinning the solver however revealed that the problem is NP-hard at least, and NP-complete at worse. An auxiliary approach was attempted whereupon we tried to map the sequence problem onto a mathematical problem with known solutions.<br />
<br />
===Software===<br />
<br />
In order to run the solver, we had to make a few assumptions. First, as we do not know what combination of sequences with att sites is part of the solution, we assume that any product in our search space is fair game for the next generation of reactions. We further assume that any plasmid with valid att sites and complementary operators is capable of self reacting and also of reacting with any other plasmid in the history of the modelled cell. Second, because of the exponential behaviour of the search space, we assume that the smallest solution that exists can be found within the search space generated after reacting 10E7 plasmids. This second assumption is made in order to have sane parameters for termination.<br />
<br />
===Math===<br />
<br />
An ancillary branch morphed out of the necessity to tend the exponential behaviour of the problem. There may exist some math that inherently facilitates the modeling and solving of this problem. We explored maths that mainly dealt with topology (knot theory) and functional reasoning (lambda theory, combinatory calculus) but finally could not identify a good candidate as a scaffold to our solution.<br />
<br />
===Results===<br />
<br />
To test the program, we ensured that it was capable of doing cassette exchange. In cassette exchange, a plasmid has a gene on interest flanked by two attB sites and the chromosome has a marker flanked by two attP sites. After enzyme-mediated recombination, the gene of interest should be in the chromosome, where the flanking sites will be changed to attL, and the marker will be in the plasmid, where the flanking sites will be changed to attR. No other products are possible after this reaction has run to completion. Our program was able to correctly perform the recombination and emulate the selection process on various types of selectable media.<br />
<br />
One of our team members designed a theoretical stackable recombination system. We converted this into a format usable by the program and ran it. Unfortunately, the program ran out of memory before running to steady state. After several round of optimization and running the program on a computer with 12GB of RAM provided by Dr. Moreno's lab at Wilfrid Laurier University, we were still unable to run the program to steady state.<br />
<br />
The combinatorial explosion of reaction products of the integrase reaction was far greater than anticipated. Even increasing the selection pressure beyond the point of biological possibility failed to control the combinatorial explosion.<br />
<br />
===Conclusion===<br />
<br />
Due to the sheer number of permutations that would have occurred in our given biological system, our initial assumptions upon which we built our software were incorrect. That is, given our hardware resources, it was not feasible for a brute force algorithm to reach steady state. <br />
<br />
From the beginning until our actual simulations, emphasis was placed on algorithm design rather than choice of language or underlying implementations of data structures. Because it had been empirically proven that our given solution was not sufficient, a C++ port had been initiated to maximize efficiency given a finite amount of computing power. However, at the time of writing, this has yet to be finished. Given the combinatorial explosion in the Python version, we hope that the C++ version will have better memory efficiency, but this may not be the case. If so, effort must be put into devising a new algorithm rather than into optimizing the program.<br />
<br />
Steps that the team could have taken that may have lead to our simulations reaching steady state include:<br />
<ul><br />
<li>Optimizing on the lowest level from start to finish.</li><br />
<li>Use of distributed computing techniques.</li><br />
<li>Use of a field programmable gate array (FPGA) rather than a conventional computing solution.</li><br />
<li>More exploration into devising a non-brute force algorithm.</li><br />
</ul><br />
<br />
Following the Jamboree, the modeling team is likely to seek to solutions in two avenues: optimizing our current algorithm, be it in Python or otherwise, and continue searching non-obvious rigorous methods to compute a biological systems steady state.</div>Jlapointe