Team:Heidelberg/NRPSDesigner

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                        <h1><span style="font-size:180%;color:#074E0B;">NRPS-Designer.</span><span class="text-muted" style="font-family:Arial, sans-serif; font-size:100%"> Designing custom peptides.</span></h1>
                        <p>This tool allows you to design any customized peptide you can build using the most common NRPS domains. This gives you the oppurtunity to include non-proteinogenic amino acids and secondary modifications without going through chemical synthesis or tRNA reprogramming. On top of providing you with a target pathway sequence the tool is also integrated with the parts registry to include any further BioBricks and with Gibthon to directly go from NRP design to Gibson cloning strategy within 10 minutes.</p>
                        <p>You should also read our <a href="https://2013.igem.org/Team:Heidelberg/Project_Software">documentation</a> and our <a href="https://2013.igem.org/Team:Heidelberg/RFCs"><b>RFC100</b></a>!
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                                  <h1>Week 12</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">In this week we implemented a first draft of the NRPS-Designer algorithm in C++ and designed a databse structure, as well as some scripts for entry making</p>
                         
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                                  <h1>Week 13</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">While revising the database structure and the input interface we integrated pfam for semi-automated domain prediction.</p>
                                  
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                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Since we noticed, that writing the whole interface ourselves will be very nasty and time-consuming we put our whole concept into the framework Django. Meanwhile our database design evolved further an the pfam integration was improved.</p>
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                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Besides the regular changes to the database design, we integrated the graphical user interface in Django and also included OpenBable for displaying chemical structures. Furthermore we visualised our concept this week.</p>
                                  
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                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">This week we mainly made changes to the NRP-Design interface and integrated ajax.</p>
                                 
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                                  <h1>Week 17</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Besides fixing the relations in our database and improving th interface, we integrated Gibthon - the tool for Gibson primer design developed by the 2011 Cambridge team.</p>
                                  
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                                  <h1>Week 18</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">This week we started filling our database, using the NRPS-PKS database. Besides that we introduced session data and updated the designer algorithm.</p>
                                 
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                                  <h1>Week 19</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">As we noticed, that different prediction tools give different domain borders, we further evaluated them and finally integrated antiSMASH</p>
                                 
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                                  <h1>Week 20</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">This week we started the manual sequence annotation and database curation and integrated the multiple sequence alignment in the database input interface.</p>
                                 
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                                  <h1>Week 21</h1>
                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">During this week we integrated our tool with the parts regisrty, did more manual database curation, added more hidden Markov-Models to antiSMASH and improved Gibthon.</p>
                                  
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                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">In order to do request management we introduced celery to our system. Furthermore we optimised the multiple sequence alignment and did lots of manual database curation.</p>
                                 
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                                  <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">In the final week we added several linkouts, including SBOL and GenBank files and fixed lots of bugs.</p>
                                  
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                <h2>Methods:</h2>
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                              Please see our documentation for our final results.
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After the Regional Jamboree in Lyon, we fixed several bugs and most important we introduced a library function. This allows for construction of many similar NRPs at a time, which could for example be useful for medical compund screening.
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