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| | {{:Team:Amsterdam/Header}} | | {{:Team:Amsterdam/Header}} |
| | + | __NOTOC__ |
| | =Collaboration= | | =Collaboration= |
| - | Synthetic Biology is an important but still controversial scientific discipline. Most of the people still don’t know what we can truly do with it. They think synthetic biology is a dangerous field and only entails risks. But Synthetic Biology has many positive applications as well.
| + | <html><img src="https://static.igem.org/mediawiki/2011/4/47/Shaking_hands.jpg"; align="right"; width="100 px"; height="100 px"; img style="margin-left: 10px;" "margin-bottom:10px"/>Worldwide 167 teams participate in this competition. We try to collaborate with them as much as possible. Helping each other will improve the research of all the teams. This collaboration has taken on many different forms: from having social gatherings with the other Dutch teams to sharing Bio bricks with teams. <br><br> |
| - | In order to dispose this negative image it’s important to share the results and experiences with other people. Not only with other scientists but also with people who have no knowledge about this type of research.
| + | On this part of the site you find the different collaborations we had with the other teams. |
| | | | |
| - | Worldwide 167 teams participate in this competition. We try to collaborate with them as much as possible. Helping each other will improve the research of all the teams. This collaboration has taken on many different forms: from having social gatherings with the other Dutch teams to sharing Bio bricks with other teams. On this part of the site you find the different collaborations we had with the other teams.
| + | <h2>List of collaborations</h2> |
| - | | + | <ul> |
| - | ==Software feedback== | + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Kick-off"><li>Kick-off with Delft</a></li> |
| - | ===Superparts construction software=== | + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Dutch_teams"><li>Meeting with the Dutch teams</a></li> |
| - | The ''Wageningen iGEM 2011'' team has been so kind to provide us with the opportunity to beta test their superparts construction software. This tool allows you to plan your superpart construction using the readily available parts in the parts registry. The software algorithm calculates the least amount of cloning that is needed to assemble the desired construct. Although the software is still beta, we’ve tried the software and made a small list of feedback.
| + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Software_Feedback"><li>Software Feedback</a> |
| - | ====GUI==== | + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Construct_Verification"><li>Construct Verification</a> |
| - | Although the software is still in development, there are a few things that we feel would greatly improve the usability of the program
| + | </li> |
| - | *Inserting the several parts is easier if they are separated by spaces.
| + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Yale"><li>Yale</a></li> |
| - | *Making double click possible on textbox
| + | </li> |
| - | *An graphical representation of the parts/modules that have been inserted. Preferable in the part registry style: <html><img src ="http://partsregistry.org/images/partbypart/icon_terminator.png"></html>. This graphical representation makes it easier to visualize what you’re working with and in case you forgot something easier to spot.
| + | <a href="https://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Meeting"><li>Meeting of Young Minds</a></li> |
| - | *A save/load function for the current modules and settings.
| + | </ul> |
| - | *Remove the DOS window and make the history box the box where the log is displayed.
| + | </html> |
| - | *Also, when making the process threaded, if possible, implement a loading bar/time remaining.
| + | |
| - | | + | |
| - | ====Construct output file====
| + | |
| - | *Here, spaces would also increase the readability of the program. If you choose to make this also a very graphical appealing file you could also export the results as a pdf file and include the graphical representation mentioned earlier.
| + | |
| - | *Clear indication of the parts of the superpart that you can make with the selected modules and which are missing. Making the missing parts a bold, or, if you make a different kind of file use colors.
| + | |
| - | | + | |
| - | ====Logarithm==== | + | |
| - | *Overall, we’re impressed with the output that is generated by the program. For example, when using the following parts….
| + | |
| - | **BBa_R0010BBa_B0034BBa_E0020BBa_B0012BBa_B0011
| + | |
| - | **BBa_R0010BBa_B0034BBa_E0040BBa_B0012BBa_B0011
| + | |
| - | **BBa_R0010BBa_B0034BBa_K361000BBa_B0012BBa_B0011
| + | |
| - | *A very satisfying result is generated. However, these are relatively simple constructs, with the only variable being the protein that is being generated and all parts are in the registry. When changing one of the double terminators around..(BBa_B0012 into BBa_B0011 and vice versa) the program freezes. As such it appears that the program is very “freeze/crash-prone” when giving sequences that it cannot solve. Threading the program and allowing you to see the log file that is being generated seems to be very helpful!
| + | |
| - | | + | |
| - | ====Overall====
| + | |
| - | The program seems very handy in order to find the quickest way to construct your superpart. Even as beta, and giving you insert valid modules the program allows you to see easily the cloning steps needed to construct your part. Main improvements that can be made at the moment from our perspective is the usability of the program, mainly when inserting modules and/or the graphical representation. Also an save/load featured is greatly appreciated. We’re very anxious to see what the next versions will bring!
| + | |
| | {{:Team:Amsterdam/Footer}} | | {{:Team:Amsterdam/Footer}} |
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Worldwide 167 teams participate in this competition. We try to collaborate with them as much as possible. Helping each other will improve the research of all the teams. This collaboration has taken on many different forms: from having social gatherings with the other Dutch teams to sharing Bio bricks with teams. 
