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Team:Heidelberg/Notebook/iGEM42
From 2013.igem.org
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 3</h1> | <h1>Week 3</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">During this week and the previous ones the whole idea of this human practices project and the code for it evolved. Thus we start out with several scrapy spiders and initial implementations of data display, text analysis and the first interesting findings on our private github repository. During this week the main task was to fix the several scraping scripts and expand them to generate more data.</p> |
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 6</h1> | <h1>Week 6</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">After thinking about how to ideally put our data into a nice homepage, we decided to use the R-package shiny. After reading into how that actually works Nikos was the one to make the first step and implement our scatter-plot app.</p> |
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 8</h1> | <h1>Week 8</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Since we had a more elaborate app layout in mind and only few people were willing to do it with bootstrap, we had to look into ways of creating an individual app without using this. The funny thing is that we ended up with bootstrap all over our wiki and out software tools - including this one.</p> |
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 9</h1> | <h1>Week 9</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">During this week we started doing real progress. The second app - the timeline - was impelmented, we created a homepage draft and managed to include the apps using iframes and finally we also started doing the text mining on the abstracts of the teams.</p> |
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 10</h1> | <h1>Week 10</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">This week we had a non-sunny sunday indoors programming all day with the goal to finish the whole project. As it turned out in the end this was way too ambigous. Nevertheless we reimplemented our scoring function, created several different homepage designs, continued the text mining and generated a set of raw filtering functions. After this sunday we all focused on a different project or on our bachelor theses.</p> |
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 15</h1> | <h1>Week 15</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">After a long break full of work we slowly started to finsih on this project and implemented a draft for the topics app.</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 18</h1> | <h1>Week 18</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"></p> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Since we still didn't have the functional filter, they were fixed. Thus we could now start exploring the data we generated and unfortunately we noticed, that part of the data was wrong or not passed through the filters correctly. So we started fixing bugs...</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 19</h1> | <h1>Week 19</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">In this week we found out that using external stylesheets and javascript together with the R code for the apps is easier than we thought. Thus we did some restyling and put the filters into a notebook. In parallel we worked on the data completion.</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 20</h1> | <h1>Week 20</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">Now that we finally understood how many opportunities shiny offers, we generated new apps, added a tabular output of the teams and added more filter functions. These also include a filter for the team name. Unfortunately it turned out, that the methods extraction is anything but mature.</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 22</h1> | <h1>Week 22</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">This week we took a closer look at the methods. We went through prominent iGEM teams and addedmethods to our list, that could actually be found in the abstracts.</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
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<div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | <div class="carousel-caption scrollContent2" data-spy="scroll" data-target="#navbarExample" data-offset="0"> | ||
<h1>Week 23</h1> | <h1>Week 23</h1> | ||
| - | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;"> | + | <p style="font-size:10pt; text-align:justify; position:relative; margin-left:6%;">The week before wiki freeze - we did lots of style adjustments and added many details to our apps in order to present a fully developed tool. To actually use the tool you can now just click on the link above this box.</p> |
<p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | <p><a class="btn btn-large btn-primary" href="#">Browse gallery</a></p> | ||
</div> | </div> | ||
Revision as of 20:57, 3 October 2013
Project
Notebook
Human Practice
iGEM 42. The answer to everything.
Have you ever easily found the piece of information you wanted from past iGEM competitions? Right! That turned out to be very hard.
Maybe you should try this tool which was developed to do exactly this: Lead you directly to the information you want.
Week 3
During this week and the previous ones the whole idea of this human practices project and the code for it evolved. Thus we start out with several scrapy spiders and initial implementations of data display, text analysis and the first interesting findings on our private github repository. During this week the main task was to fix the several scraping scripts and expand them to generate more data.
Week 4
Week 6
After thinking about how to ideally put our data into a nice homepage, we decided to use the R-package shiny. After reading into how that actually works Nikos was the one to make the first step and implement our scatter-plot app.
Week 8
Since we had a more elaborate app layout in mind and only few people were willing to do it with bootstrap, we had to look into ways of creating an individual app without using this. The funny thing is that we ended up with bootstrap all over our wiki and out software tools - including this one.
Week 9
During this week we started doing real progress. The second app - the timeline - was impelmented, we created a homepage draft and managed to include the apps using iframes and finally we also started doing the text mining on the abstracts of the teams.
Week 10
This week we had a non-sunny sunday indoors programming all day with the goal to finish the whole project. As it turned out in the end this was way too ambigous. Nevertheless we reimplemented our scoring function, created several different homepage designs, continued the text mining and generated a set of raw filtering functions. After this sunday we all focused on a different project or on our bachelor theses.
Week 15
After a long break full of work we slowly started to finsih on this project and implemented a draft for the topics app.
Week 18
Since we still didn't have the functional filter, they were fixed. Thus we could now start exploring the data we generated and unfortunately we noticed, that part of the data was wrong or not passed through the filters correctly. So we started fixing bugs...
Week 19
In this week we found out that using external stylesheets and javascript together with the R code for the apps is easier than we thought. Thus we did some restyling and put the filters into a notebook. In parallel we worked on the data completion.
Week 20
Now that we finally understood how many opportunities shiny offers, we generated new apps, added a tabular output of the teams and added more filter functions. These also include a filter for the team name. Unfortunately it turned out, that the methods extraction is anything but mature.
Week 22
This week we took a closer look at the methods. We went through prominent iGEM teams and addedmethods to our list, that could actually be found in the abstracts.
Week 23
The week before wiki freeze - we did lots of style adjustments and added many details to our apps in order to present a fully developed tool. To actually use the tool you can now just click on the link above this box.
Methods:
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