http://2009.igem.org/wiki/index.php?title=Special:Contributions/Plee&feed=atom&limit=50&target=Plee&year=&month=2009.igem.org - User contributions [en]2024-03-29T01:24:39ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:Johns_Hopkins-BAG/TeamTeam:Johns Hopkins-BAG/Team2009-10-07T21:02:22Z<p>Plee: /* Team */</p>
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== '''Team''' ==<br />
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'''Advisors:'''<br />
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*''' Jef Boeke''': A Professor at Johns Hopkins School of Medicine who studies yeast genetics and other things. He started the Synthetic Yeast Genome Project with two colleagues, Joel Bader and Srinivasan Chandrasegaran, and the help of dozens of undergraduates.<br />
*'''Eric Cooper''': Eric Cooper<br />
*'''Sarah Richardson''': I'm a fifth year graduate student of Human Genetics at the Johns Hopkins School of Medicine and a DOE Computational Science Graduate Fellow.My advisor is Dr. Joel Bader and he is wondering where my thesis is.<br />
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'''Undergrads:'''<br />
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*'''Pablo Lee ''': I'm a senior majoring in Computer Science. I was a student in the Build-a-Genome course, where I discovered the field of computational biology!<br />
*'''Wei Rose Xie''': Hi! I am a senior majoring in Molecular and Cellular Biology and minoring in Music. I am a Build-a-Genome grad and was also a Build-A-Genome mentor. Other than being on the iGEM team, I am also a campus tourguide, sing in an a cappella group, volunteer at the hospital, and participate in our student government!<br />
*'''James DiCarlo ''': Hello! I am a senior Chemical and Biomolecular Engineering major at JHU. I love synthetic biology and this is my second time competing at the iGEM Jamboree! My other main nerdy interests include, but are not limited to: horticulture, genome evolution, artificial photosynthesis and running! Exclamation points!<br />
*'''Zheyuan Guo''': I’m an undergraduate researcher at the Boeke Lab who helped implement the Ligation Chain Reaction into the Build-A-Genome course. <br />
*'''Christopher Von Dollen''': I am a senior majoring in Chemical and Bimolecular engineering and am an Army ROTC cadet. I have participated in JHU's Build-a-Genome and BAG Mentor course for two semesters.<br />
*''' Ingrid Spielman''': I'm a Senior Material Science and Engineering Student. I participated in iGEM2008 and this year I'm helping out with the wiki. Also, I enjoy collecting insects and I think that multidisciplinary sciences is the way to go. <br />
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<gallery><br />
Image:JHU_James.JPG|James<br />
Image:JHU_Yuan.JPG|Yuan<br />
Image:JHU_Sara.JPG|Sara<br />
Image:JHU_Rose.JPG|Rose<br />
Image:JHU_Boeke.JPG|Jeff Boeke<br />
Image:JHU_Ingrid.jpg|Ingrid<br />
Image:Team_.png|Christopher<br />
Image:Team_.png|Pablo<br />
Image:Team_.png|Eric<br />
</gallery><br />
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{{Template:JHU_BAG_Bottom}}</div>Pleehttp://2009.igem.org/Team:Johns_Hopkins-BAG/Software_ToolsTeam:Johns Hopkins-BAG/Software Tools2009-10-01T20:02:07Z<p>Plee: /* Software Tools */</p>
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<div>{{Template:JHU_BAG_Top}}<br />
{{Template:JHU_BAG_SideBar}}<br />
==Software Tools==<br />
Both the Sc2.0 project and the Build-A-Genome course require a number of specialized software applications and editing environments,; each of these is briefly summarized here. Part of the philosophy of Build-A-Genome is to use ONLY open source software.<br />
<br />
• [http://baderlab.bme.jhu.edu:8888 Moodle] is an existing open source course management system. It was modified to function as an online lab notebook for all B-A-G students to keep track of voluminous data and monitor progress of Building Block synthesis. Things like gel images and progress reports on the Building Blocks were stored in the MOODLE, along with various resources like protocols, lectures, and articles.<br />
<br />
• CloneQC is a brand new program designed to automate the analysis of thousands of tracefiles of sequenced DNA. The somewhat complex process involved in calling whether or not the generated Building Block is an exact match to the designed Building Block was automated. The program can successfully identify exact and non-exact matches, and in some cases where it isn’t sure, it will ask a human to determine the status.<br />
<br />
• [http://baderlab.bme.jhu.edu/baderlab/index.php/BioStudio BioStudio] is a web application developed by B-A-G Team member Sarah Richardson layered on top of an existing generic genome browser called GBROWSE. BioStudio allows collaborative creation and editing of genome-sized DNA sequences, using revision control systems and most importantly, a graphical user interface, which facilitates many genome editing tasks. It provides various useful tools to aid the editor in the design, like ways to visualize the sequence at various levels of detail, or to visualize restriction site positions and recombination sites, or the percent content of certain base pairs, and so on.<br />
<br />
• [http://www.genedesign.org GeneDesign] is an existing program written by B-A-G Team member Sarah Richardson that provides tools for more specific gene or Building Block level design. Features like codon substitutions, silent site removals, restriction site design, and more are available. Most relevant to B-A-G, after the design of a gene or Building Block, tiling oligo order sheets can be automatically generated. <br />
<br />
A new database to tie all of these resources together is being put together to provide a unified database, which will give a solid base for the creation of additional custom software and web applications. It will also allow for the different pieces of software to interact with each other, which in turn will allow for a seamless pipeline system to be generated. <br />
<br />
<br />
{{Template:JHU_BAG_Bottom}}</div>Pleehttp://2009.igem.org/Team:Johns_Hopkins-BAG/Software_ToolsTeam:Johns Hopkins-BAG/Software Tools2009-09-29T01:40:18Z<p>Plee: /* Software Tools */</p>
<hr />
<div>{{Template:JHU_BAG_Top}}<br />
{{Template:JHU_BAG_SideBar}}<br />
==Software Tools==<br />
Both the Sc2.0 project and the Build-A-Genome course require a number of specialized software applications and editing environments,; each of these is briefly summarized here. Part of the philosophy of Build-A-Genome is to use ONLY open source software.<br />
<br />
• [http://baderlab.bme.jhu.edu:8888 MOODLE] is an existing open source course management system. It was modified to function as an online lab notebook for all B-A-G students to keep track of voluminous data and monitor progress of Building Block synthesis. Things like gel images and progress reports on the Building Blocks were stored in the MOODLE, along with various resources like protocols, lectures, and articles.<br />
<br />
• CloneQC is a brand new program designed to automate the analysis of thousands of tracefiles of sequenced DNA. The somewhat complex process involved in calling whether or not the generated Building Block is an exact match to the designed Building Block was automated. The program can successfully identify exact and non-exact matches, and in some cases where it isn’t sure, it will ask a human to determine the status.<br />
<br />
• BioStudio is a web application developed by B-A-G Team member Sarah Richardson layered on top of an existing generic genome browser called GBROWSE. BioStudio allows collaborative creation and editing of genome-sized DNA sequences, using revision control systems and most importantly, a graphical user interface, which facilitates many genome editing tasks. It provides various useful tools to aid the editor in the design, like ways to visualize the sequence at various levels of detail, or to visualize restriction site positions and recombination sites, or the percent content of certain base pairs, and so on.<br />
<br />
• [http://baderlab.bme.jhu.edu/gd GeneDesign] is an existing program written by B-A-G Team member Sarah Richardson that provides tools for more specific gene or Building Block level design. Features like codon substitutions, silent site removals, restriction site design, and more are available. Most relevant to B-A-G, after the design of a gene or Building Block, tiling oligo order sheets can be automatically generated. <br />
<br />
A new database to tie all of these resources together is being put together to provide a unified database, which will give a solid base for the creation of additional custom software and web applications. It will also allow for the different pieces of software to interact with each other, which in turn will allow for a seamless pipeline system to be generated. <br />
<br />
<br />
{{Template:JHU_BAG_Bottom}}</div>Pleehttp://2009.igem.org/Team:Johns_Hopkins-BAG/Software_ToolsTeam:Johns Hopkins-BAG/Software Tools2009-09-29T01:39:32Z<p>Plee: /* Software Tools */</p>
<hr />
<div>{{Template:JHU_BAG_Top}}<br />
{{Template:JHU_BAG_SideBar}}<br />
==Software Tools==<br />
Both the Sc2.0 project and the Build-A-Genome course require a number of specialized software applications and editing environments,; each of these is briefly summarized here. Part of the philosophy of Build-A-Genome is to use ONLY open source software.<br />
<br />
• [http://baderlab.bme.jhu.edu:8888 MOODLE] is an existing open source course management system. It was modified to function as an online lab notebook for all B-A-G students to keep track of voluminous data and monitor progress of Building Block synthesis. Things like gel images and progress reports on the Building Blocks were stored in the MOODLE, along with various resources like protocols, lectures, and articles.<br />
<br />
• CloneQC is a brand new program written by Pablo Lee designed to automate the analysis of thousands of tracefiles of sequenced DNA. The somewhat complex process involved in calling whether or not the generated Building Block is an exact match to the designed Building Block was automated. The program can successfully identify exact and non-exact matches, and in some cases where it isn’t sure, it will ask a human to determine the status.<br />
<br />
• BioStudio is a web application developed by B-A-G Team member Sarah Richardson layered on top of an existing generic genome browser called GBROWSE. BioStudio allows collaborative creation and editing of genome-sized DNA sequences, using revision control systems and most importantly, a graphical user interface, which facilitates many genome editing tasks. It provides various useful tools to aid the editor in the design, like ways to visualize the sequence at various levels of detail, or to visualize restriction site positions and recombination sites, or the percent content of certain base pairs, and so on.<br />
<br />
• [http://baderlab.bme.jhu.edu/gd GeneDesign] is an existing program written by B-A-G Team member Sarah Richardson that provides tools for more specific gene or Building Block level design. Features like codon substitutions, silent site removals, restriction site design, and more are available. Most relevant to B-A-G, after the design of a gene or Building Block, tiling oligo order sheets can be automatically generated. <br />
<br />
A new database to tie all of these resources together is being put together to provide a unified database, which will give a solid base for the creation of additional custom software and web applications. It will also allow for the different pieces of software to interact with each other, which in turn will allow for a seamless pipeline system to be generated. <br />
<br />
<br />
{{Template:JHU_BAG_Bottom}}</div>Pleehttp://2009.igem.org/Team:Johns_Hopkins-BAG/Software_ToolsTeam:Johns Hopkins-BAG/Software Tools2009-09-29T01:14:56Z<p>Plee: /* Software Tools */</p>
<hr />
<div>{{Template:JHU_BAG_Top}}<br />
{{Template:JHU_BAG_SideBar}}<br />
==Software Tools==<br />
Both the Sc2.0 project and the Build-A-Genome course require a number of specia-lized software applications and editing environments,; each of these is briefly summa-rized here. Part of the philosophy of Build-A-Genome is to use ONLY open source software.<br />
<br />
• [http://baderlab.bme.jhu.edu:8888 MOODLE] is an existing open source course management system. It was mod-ified to function as an online lab notebook for all B-A-G students to keep track of voluminous data and monitor progress of Building Block synthesis. Things like gel images and progress reports on the Building Blocks were stored in the MOODLE, along with various resources like protocols, lectures, and articles.<br />
<br />
• CloneQC is a brand new program written by Pablo Lee designed to automate the analysis of thousands of tracefiles of sequenced DNA. The somewhat complex process involved in calling whether or not the generated Building Block is an exact match to the designed Building Block was automated. The program can successfully identify exact and non-exact matches, and in some cases where it isn’t sure, it will ask a human to determine the status.<br />
<br />
• BioStudio is a web application developed by B-A-G Team member Sarah Rich-ardson layered on top of an existing generic genome browser called GBROWSE. BioStudio allows collaborative creation and editing of genome-sized DNA sequences, using revision control systems and most importantly, a graphical user interface, which facilitates many genome editing tasks. It provides various useful tools to aid the editor in the design, like ways to visualize the sequence at various levels of detail, or to visualize restriction site positions and recombination sites, or the percent content of certain base pairs, and so on.<br />
<br />
• [http://baderlab.bme.jhu.edu/gd GeneDesign] is an existing program written by B-A-G Team member Sarah Richardson that provides tools for more specific gne- or Building Block level de-sign. Features like codon substitutions, silent site removals, restriction site de-sign, and more are available. Most relevant to B-A-G, after the design of a gene or Building Block, tiling oligo order sheets can be automatically generated. <br />
<br />
A new database to tie all of these resources together is being put together to provide a unified database, which will give a solid base for the creation of additional custom soft-ware and web applications. It will also allow for the different pieces of software to inte-ract with each other, which in turn will allow for a seamless pipeline system to be generated. <br />
<br />
<br />
{{Template:JHU_BAG_Bottom}}</div>Plee