http://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&feed=atom&action=historyTeam:Newcastle/E-Science - Revision history2024-03-28T14:04:27ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=196745&oldid=prevRachelBoyd: /* Motivation: */2010-10-27T21:10:55Z<p><span class="autocomment">Motivation:</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|Synthetic Biology is the engineering of biological entities to perform novel and desirable functions. Synthetic biologists already make use of computational resources to a large extent which can be seen by the software tools such as CLONEQC, Biskit and Internet based repositories such as the MIT Biobrick library at http://partsregistry.org/Main_Page. In both Systems and Synthetic Biology analysis consists of researchers taking the outputs from some software and feeding it to the inputs of other software. This pipeline or workflow can be computerised by using software such as Taverna. Research into the application of computerised workflows to Synthetic Biology has revealed the paucity of published material in this area. Therefore, this has been identified as an opportunity for research and possible development of tools, which could greatly enhance methodologies and workflows in Synthetic Biology. We show how an e-Science approach, i.e. the utilisation of advanced computing resources and technologies to support scientists, benefits the Synthetic Biology engineering process. We further propose a development life-cycle and show how this approach can improve the design of synthetic biological entities.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|Synthetic Biology is the engineering of biological entities to perform novel and desirable functions. Synthetic biologists already make use of computational resources to a large extent which can be seen by the software tools such as CLONEQC, Biskit and Internet based repositories such as the MIT Biobrick library at http://partsregistry.org/Main_Page. In both Systems and Synthetic Biology analysis consists of researchers taking the outputs from some software and feeding it to the inputs of other software. This pipeline or workflow can be computerised by using software such as <ins class="diffchange diffchange-inline">[http://www.taverna.org.uk/ </ins>Taverna<ins class="diffchange diffchange-inline">]</ins>. Research into the application of computerised workflows to Synthetic Biology has revealed the paucity of published material in this area. Therefore, this has been identified as an opportunity for research and possible development of tools, which could greatly enhance methodologies and workflows in Synthetic Biology. We show how an e-Science approach, i.e. the utilisation of advanced computing resources and technologies to support scientists, benefits the Synthetic Biology engineering process. We further propose a development life-cycle and show how this approach can improve the design of synthetic biological entities.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Newcastel_workflows_Synbio001.png|thumb|Motivation ]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:Newcastel_workflows_Synbio001.png|thumb|Motivation ]]</div></td></tr>
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</table>RachelBoydhttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=184051&oldid=prevJannetta at 14:23, 27 October 20102010-10-27T14:23:40Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[E-Science_References]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[E-Science_References]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">|-}</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:Newcastle/footer}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Team:Newcastle/footer}}</div></td></tr>
</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=183989&oldid=prevJannetta at 14:21, 27 October 20102010-10-27T14:21:48Z<p></p>
<a href="http://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=183989&oldid=118142">Show changes</a>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=118142&oldid=prevSwoodhouse: E-Science moved to Team:Newcastle/E-Science2010-10-21T22:19:36Z<p><a href="/E-Science" class="mw-redirect" title="E-Science">E-Science</a> moved to <a href="/Team:Newcastle/E-Science" title="Team:Newcastle/E-Science">Team:Newcastle/E-Science</a></p>
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</tr></table>Swoodhousehttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113634&oldid=prevJannetta: /* Putting it all together */2010-10-20T14:42:44Z<p><span class="autocomment">Putting it all together</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 1 (This image is 1.1 MB and might take a while to download.)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 1 (This image is 1.1 MB and might take a while to download.)</div></td></tr>
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</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113626&oldid=prevJannetta at 14:40, 20 October 20102010-10-20T14:40:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=Discussion:=</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Synthetic Biology is a very young field of study and still lacks the methodologies already established in other fields of engineering. To speed up the process of putting these methodologies in place, it makes sense to borrow from the other engineering disciplines. Systems biology already makes use of an e-Science approach using computerised workflows with great success. The approach serves to avoid tedious cutting and pasting of retrieved result from one software package to the next and thus saves significant amounts of time and effort to improve efficiency and accuracy.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Using the bottom-up approach to design, means that design starts with the most simple of identifiable parts, working its way up to a complex system composed of these parts (Cooling et al., 2010). This approach relates very closely to the development of software and fits in very well with a design and development approach similar to the software development life cycle. Thus, we proposed a Synthetic Biology life cycle which, apart from one phase, is almost identical to the SDLC.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The subtilin receiver model created by Cooling et al. (2010) provided all the virtual parts necessary for this research project. Creating a graphical representation of the model allowed us to identify the motifs which provided the first level of abstraction and encapsulation. The principles of abstraction and encapsulation were borrowed from software and serve the purpose of hiding the complexity of a design (Henderson-Sellers, 1997). Models consist not only of physical parts, but also need non-physical parts that glue the physical parts together for simulation purposes. These physical and non-physical parts provide the minimal parts required in the bottom-up approach. The rules for putting these parts together were captured in a database which allowed us to query the database for a series of parts in the correct order almost ready for simulation. Once the parts are extracted from the database according to the rules, programmatically extract the units that need to be specified in the model and the connections that need to be made between parts. A naming convention which allowed us to determine which variables from which parts need connecting. An alternative approach would be to extend the database to hold the information required for mapping parts and variables. This approach would simplify the creation of the CellML parts, but would complicate the design of the software and database.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">With the database in place and populated we developed a RESTful web service that extracts the parts required for a requested motif, assemble the motif and returns it in CellML as a simulatable model. The service can return the CellML to the client, but it can also simulate the model using JSim, a Java based software application. Three services, a database service, a web service and a simulating service were established. Finally a Taverna workflow was created that use these services in order to create a generic simulatable model. The parts of the generic model can, for the moment, be replaced manually with specific parts. Ideally the service should be extended to replace parts automatically so that minimal input is required from the user.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Although all of the above mentioned services were installed on one server it is possible to develop these services such that they can be run on different servers and off course in different locations on the Internet.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">A variation on the waterfall software development life cycle was suggested and it was illustrated how this method can successfully be used to guide the design process. It is, however, a very old method and software engineering has produced many alternatives since. It would be worth while investigating some of the newer methods that might prove to be even more successful if applied to the Synthetic Biology development life cycle.</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==Putting it all together==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Figure 1 shows, from start to finish, the internal flow of information in an ideal workflow that would produce a complete and simulated model of the requested part or motif. The workflow includes the workflows already created as well as the services provided by BioBrickIt. To actually be able to implement the complete workflow both BioBrickIt and the Taverna workflows created will need extending.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The process is started with input by the user (Figure 1(a)), specifying which motif and which specific parts are required.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The next step. (Figure 1(b)), is to retrieve the motif with generic parts from the database. The motif is composed of virtual part and assembled according to the rules which are also capture in the database. This motif is simulatable as is, but contains no specific parts as yet.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Step 3, (Figure 1(c)), uses a service, such as BioBrickIt, that can use the generated motif and replace generic virtual parts with specified parts of the same type. For instance, a generic constitutive promoter can be replaced by pspaRK.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Step 4, (Figure 1(d)), uses a service such as JSim to simulate the model. To make sense of the simulation results it is usually required to visualise it in some form. Visualisation is done in step 5.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Step 5, (Figure 1(e)), produces human readable formats of the simulation results. Visualisation is usually in the format of graphs.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Step 6, (Figure 1(f)), is the production of a BioBrick sequence from the produced model produced in step 3. Newcastle University is currently researching such a model-to-sequence conversion algorithm. This step would make use of the GetVPSequence and GetSites workflows, to retrieve physical part sequences and check them for specified restriction sites.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Step 7, (Figure 1(g)), show the possible results that can be produced by the workflow.</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Figure 1 (This image is 1.1 MB and might take a while to download.)</ins></div></td></tr>
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</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113606&oldid=prevJannetta at 14:34, 20 October 20102010-10-20T14:34:59Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A MySQL relational database was designed and implemented to hold both physical and non-physical parts. The database was populated manually and using the file upload feature of the BioBrickIt web service. A set of generic parts was all that was required for this research, but the database contains several other parts which are available from the 2008 iGEM Subtilin receiver. The database is online and can be accessed via the BioBrickIt Service at http://msc.jannetta.com:8080/BioBrickIt/.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A MySQL relational database was designed and implemented to hold both physical and non-physical parts. The database was populated manually and using the file upload feature of the BioBrickIt web service. A set of generic parts was all that was required for this research, but the database contains several other parts which are available from the 2008 iGEM Subtilin receiver. The database is online and can be accessed via the BioBrickIt Service at http://msc.jannetta.com:8080/BioBrickIt/.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>JSim server</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==</ins>JSim server<ins class="diffchange diffchange-inline">==</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>When accessing the BioBrickIt service on http://msc.jannetta.com:8080/BioBrickIt/, a simulation of the generated motif can be requested. This is done by adding simulate=yes as a parameter to the URL. For example requesting a simulation of the generic constitutive promotor can be obtained with: http://msc.jannetta.com:8080/BioBrickIt/GetMotifModel?motif_name=motif_constitutive_promoter&simulate=yes.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>When accessing the BioBrickIt service on http://msc.jannetta.com:8080/BioBrickIt/, a simulation of the generated motif can be requested. This is done by adding simulate=yes as a parameter to the URL. For example requesting a simulation of the generic constitutive promotor can be obtained with: http://msc.jannetta.com:8080/BioBrickIt/GetMotifModel?motif_name=motif_constitutive_promoter&simulate=yes.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taverna workflows</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==</ins>Taverna workflows<ins class="diffchange diffchange-inline">==</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used Taverna Workbench to create 3 workflows. The first workflow (Figure 3) makes use of the BioBrickIt Webservice to determine the presence of restriction sites in a provided sequence.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We used Taverna Workbench to create 3 workflows. The first workflow (Figure 3) makes use of the BioBrickIt Webservice to determine the presence of restriction sites in a provided sequence.</div></td></tr>
</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113602&oldid=prevJannetta: /* Motifs */2010-10-20T14:34:00Z<p><span class="autocomment">Motifs</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The motifs were identified using the Subtilin receiver model created by the Newcastle University iGEM team of 2008.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The motifs were identified using the Subtilin receiver model created by the Newcastle University iGEM team of 2008.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The BioBrickIt Web Service</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==</ins>The BioBrickIt Web Service<ins class="diffchange diffchange-inline">==</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We developed a RESTful web service which we called BioBrickIt. It is available online at http://msc.jannetta.com:8080/BioBrickIt. BioBrickIt was developed using J2EE web technologies, JAXP for XML handling, the Apache Tomcat web server and a mySQL database. The service and its source code can also be downloaded as a .war file from http://msc.jannetta.com:8080/BioBrickIt/BioBrickIt.war.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We developed a RESTful web service which we called BioBrickIt. It is available online at http://msc.jannetta.com:8080/BioBrickIt. BioBrickIt was developed using J2EE web technologies, JAXP for XML handling, the Apache Tomcat web server and a mySQL database. The service and its source code can also be downloaded as a .war file from http://msc.jannetta.com:8080/BioBrickIt/BioBrickIt.war.</div></td></tr>
</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113594&oldid=prevJannetta at 14:27, 20 October 20102010-10-20T14:27:35Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Workflow 1, Restriction site finder. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Workflow 1, Restriction site finder. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Workflow2.png<del class="diffchange diffchange-inline">|800px</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Workflow2.png]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: Workflow 2, Retrieve sequences of virtual parts. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: Workflow 2, Retrieve sequences of virtual parts. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Workflow3.png<del class="diffchange diffchange-inline">|800px</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Workflow3.png]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td></tr>
</table>Jannettahttp://2010.igem.org/wiki/index.php?title=Team:Newcastle/E-Science&diff=113591&oldid=prevJannetta at 14:27, 20 October 20102010-10-20T14:27:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We identified two motifs, a constitutive promoter motif and a coding sequence motif (see Figures 1 and 2)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We identified two motifs, a constitutive promoter motif and a coding sequence motif (see Figures 1 and 2)</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 1: The constitutive promoter motif. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 1: The constitutive promoter motif. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Motif2.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Newcastle_workflows_Motif2.png<ins class="diffchange diffchange-inline">|800px</ins>]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2: The coding sequence motif.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2: The coding sequence motif.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The second workflow (Figure 4) retrieves the sequences of provided physical parts using the BioBrickIt service. It then concatenates the sequences. The intension is that this workflow be extended or embedded in a larger workflow that could conver a CellML model to a sequence.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The second workflow (Figure 4) retrieves the sequences of provided physical parts using the BioBrickIt service. It then concatenates the sequences. The intension is that this workflow be extended or embedded in a larger workflow that could conver a CellML model to a sequence.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Workflow 1, Restriction site finder. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 3: Workflow 1, Restriction site finder. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: Workflow 2, Retrieve sequences of virtual parts. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 4: Workflow 2, Retrieve sequences of virtual parts. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 5: Workflow 3, Retrieve simulatable CellML model of a motif. </div></td></tr>
</table>Jannetta