Team:Washington/Tools Created/New Software

From 2010.igem.org

(Difference between revisions)
(→Update 11/30/2010:This page will be locked soon, so be sure to visit the TinkerCell and PartsRobot sites for more current information.)
 
(115 intermediate revisions not shown)
Line 1: Line 1:
-
{{Template:Team:Washington/Templates/Header}}
+
{{Template:Team:Washington/Templates/Header}}<html><script type="text/javascript">
-
<html>
+
-
<script type="text/javascript">
+
$(function() {
$(function() {
   var mainimg = document.getElementById("mainimg");
   var mainimg = document.getElementById("mainimg");
Line 21: Line 19:
   }, restore_mainimg);
   }, restore_mainimg);
});
});
-
</script>
+
</script></html>__NOTOC__As synthetic biologists create ever more complex systems, automation and computer-aided design are becoming indispensable. Computational tools will eventually play a central role in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the University of Washington 2010 iGEM team has developed a standard for the electronic distribution of diagrams, detailed in [[Team:Washington/Tools_Created/New_Software#A Standard for Electronic Diagrams|BBF RFC 68]]. We also created two new software tools: [[Team:Washington/Tools_Created/New_Software#wikidust|WikiDust]] and [[Team:Washington/Tools_Created/New_Software#partsrobot|PartsRobot]].
-
</html>
+
-
<!---------------------------------------PAGE CONTENT GOES BELOW THIS---------------------------------------->
+
-
__NOTOC__
+
-
<span id="wikidust">
+
-
As synthetic biologists create ever more complex systems, automation and computer-aided design are becoming indispensable. Computational tools will eventually play a central role in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the Washington 2010 iGEM team has developed a standard for the electronic distribution of diagrams, as well as two new software tools.
+
-
==Standard Diagrams==
+
===Update 11/30/2010:<br />This page will be locked soon, so be sure to visit the [http://www.tinkercell.com/plugins/wikidust WikiDust] and [http://sourceforge.net/p/partsrobot/home/ PartsRobot] sites for more current information.===
-
Distribution of a standardized diagrams describing DNA construct designs for synthetic biology depends both on the use of a standard set of symbols and on the method of distribution. Therefore the two main requirements for BBF RFC 64 are:
+
-
  1. The use of SBOLv symbols
+
-
  2. The linking of symbols to reference entry pages on the Registry of Standard Biological Parts using http URLs
+
-
Essentially creating a systematically annotated image, using the <imagemap> HTML tag. The result constitutes a diagram which allows the reader to click on portions of the diagram which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram.  
+
-
<!-- >>>>>>>>>add something about why sharing/dissemination/publication is important. Then Introduce TinkerCell and The Registry. -->
+
<span id="wikidust">
-
<br />
+
==[[Image:wikidust_banner.png|500px|center]]==
==[[Image:wikidust_banner.png|500px|center]]==
 +
====<center>A Standard for Electronic Diagrams</center>====
 +
Standard, unambiguous diagrams are central to communication in many established fields of engineering, but have not yet been widely adopted by synthetic biologists. Through the use of diagrams based on SBOL-visual ([http://bbf.openwetware.org/RFC.html#BBF_RFC_16:_Synthetic_Biology_Open_Language_Visual_.28SBOLv.29_Specification BBF RFC 16]) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. Usefulness of shared diagrams depends both on a standard set of symbols and on the method of distribution. Therefore the two main requirements for our proposed standard, [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_68:_Standard_for_the_Electronic_Distribution_of_SBOLv_Diagrams BBF RFC 68], are:
 +
# The use of SBOLv symbols
 +
# The linking of symbols to reference entry pages on the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts] using http URLs
 +
In the resulting diagram, the reader can click on portions which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram. This makes research easier and promotes better part descriptions.
 +
<br />
-
WikiDust is a plugin for [[Team:Washington/Tools Used/Software#tinkercell|TinkerCell]], a computer-aided design tool developed here at the University of Washington. WikiDust can be used to export TinkerCell models to the iGEM wiki or other webpages. Other users can then download the models for use in their own larger system, or explore how the model responds to parameter changes. Our goal in creating WikiDust is to provide an easy way to share models and to encourage iGEM teams and researchers to describe their parts quantitatively. This, in turn, will help others reuse the devices in the future projects.
+
====<center>Software to Create and Share Standards-Compliant Diagrams</center>====
 +
WikiDust is a plugin for [[Team:Washington/Tools Used/Software#tinkercell|TinkerCell]], a computer-aided design tool developed here at the [http://www.washington.edu/ University of Washington]. WikiDust can be used to export diagrams of TinkerCell models to the iGEM wiki or other webpages. Our goal in creating WikiDust is to provide an easy way to share models and to encourage iGEM teams and researchers to describe their parts more completely. This, in turn, will help others reuse them in future projects.
[[Image:washington_rightclick.png|200px|left]][[Image:uw_sauro_linkpanel.png|300px|left]]
[[Image:washington_rightclick.png|200px|left]][[Image:uw_sauro_linkpanel.png|300px|left]]
-
<br />
+
 
-
<!-- >>>>>>>For example from a repository of standard virtual parts...  cite: (Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Cooling 2010) -->
+
One thing WikiDust does is provide a method to associate TinkerCell items, such as promoters or coding sequences, with parts on the Registry. The same mechanism could also be extended in the future to download reaction kinetics and other parameters from sources like the [http://www.ncbi.nlm.nih.gov/pubmed/20160009 Standard Virtual Parts Repository] or the [http://www.ncbi.nlm.nih.gov/pubmed/16381960 Biomodels Database]. For now though, it demonstrates the feasability of using the publicly available [http://www.sbolstandard.org Standard Biological Parts Knowledgebase (SBPkb)] to retrieve part information using Semantic Web standards.
-
The first thing WikiDust does is provide a method to associate TinkerCell items with parts on the registry. The same mechanism could also be extended in the future to download additional descriptions, such as reaction kinetics, of the items into TinkerCell. For now though, it demonstrates the feasability of using a [http://www.sbolstandard.org publicly available semantic knowledgebase] to retrieve part information.
+
<br />
<br />
<br />
<br />
Line 59: Line 53:
<br />
<br />
<br />
<br />
-
<br />
+
To associate a link with an item in TinkerCell, right click on it and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one. Click "Use Selected" to choose one from the list, or enter your own link and click "Use Custom".
-
 
+
-
To associate a link with an item in TinkerCell, right click on it and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one.
+
<br />
<br />
<br />
<br />
-
After the model of your device or system is finished, and you've added all the links you want, you can upload a representation of it to your page. Just choose "Create Imagemap" from the TinkerCell plugins menu, and change any options you want in the window that pops up. WikiDust will automatically handle uploading to the iGEM wiki, or it can just display code for you to copy and paste to another site. Clicking an item in the uploaded diagram will go to the correct part page. In fact, [https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram our Tse2/Tsi2 diagram] was generated using WikiDust.  
+
After the model of your device or system is finished, and you've added all the links you want, you can upload a diagram of it to a webpage. Just choose "Create Imagemap" from the TinkerCell plugins menu, and change any options you want in the window that pops up. WikiDust will automatically handle uploading to the iGEM wiki, or it can just display code for you to copy and paste to another site. The diagram will be interactive; clicking an item will take you to the correct part page. In fact, [https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram our tse2/tsi2 diagram] was generated using WikiDust.
<!-- [[Image:uw_sauro_model_on_wiki.png|500px|left]] -->
<!-- [[Image:uw_sauro_model_on_wiki.png|500px|left]] -->
<!--[https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram https://static.igem.org/mediawiki/2010/4/44/Washington_Diagram_F2620_Tse2_Tsi2_2.png]-->
<!--[https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram https://static.igem.org/mediawiki/2010/4/44/Washington_Diagram_F2620_Tse2_Tsi2_2.png]-->
<br />
<br />
-
'''To start using WikiDust, [http://www.tinkercell.com/downloads-2 download TinkerCell]. It will automatically keep you up to date with the latest version.'''
+
 
 +
'''To start using WikiDust you’ll need the main TinkerCell program, as well as Python and Subversion. All three can be found on the [http://www.tinkercell.com/downloads-2 TinkerCell download page].'''
</span>
</span>
<span id="partsrobot">
<span id="partsrobot">
Line 78: Line 71:
==[[Image:partsrobot_banner.png|500px|center]]==
==[[Image:partsrobot_banner.png|500px|center]]==
 +
====<center>Registry Submission Made Easy</center>====
-
 
+
PartsRobot is a command-line tool that can submit many parts to the [http://partsregistry.org/Main_Page Registry] at once. This makes it fast and easy to enter information about a series of similar parts&mdash;promoters of different strengths, variations on a protein, etc.
-
We have also developed a command-line tool to submit multiple parts to the [http://partsregistry.org/Main_Page Registry] at once. This will make it much easier and faster to submit a series of similar parts&mdash;promoters of different strengths, variations on a protein, etc. We used it to submit most of our parts.
+
<br />
<br />
<br />
<br />
Line 113: Line 106:
<code>python partsrobot.py submit yourspreadsheet.csv </code>
<code>python partsrobot.py submit yourspreadsheet.csv </code>
-
<br />
+
<font size=1>
-
The program will log into the Registry and check your parts for syntax errors. Then, after you give the go-ahead, it will submit them.
+
(Exact command varies with OS and file locations. See the README for details.)
 +
</font>
 +
 
 +
Once launched, the program will log into the Registry and check your parts for syntax errors. After you give the go-ahead, it will submit them. Most of [[Team:Washington/Parts|our parts]] were submitted this way.
<br />
<br />
-
'''Get PartsRobot from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page].'''
+
'''You can download PartsRobot from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page].'''
<br clear=both>
<br clear=both>
 +
<br />
</span>
</span>
 +
<!---------------------------------------PAGE CONTENT GOES ABOVE THIS---------------------------------------->
<!---------------------------------------PAGE CONTENT GOES ABOVE THIS---------------------------------------->
<div style="text-align:center">
<div style="text-align:center">
'''&larr; [[Team:Washington/Tools Created/New Vectors|New Vectors]]'''
'''&larr; [[Team:Washington/Tools Created/New Vectors|New Vectors]]'''
&nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp;
-
'''[[Team:Washington/Tools Used|Tools Used]] &rarr;'''
+
'''[[Team:Washington/Tools Used|Overview of Tools We Used]] &rarr;'''
</div>
</div>
{{Template:Team:Washington/Templates/Footer}}
{{Template:Team:Washington/Templates/Footer}}

Latest revision as of 17:31, 6 December 2010

As synthetic biologists create ever more complex systems, automation and computer-aided design are becoming indispensable. Computational tools will eventually play a central role in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the University of Washington 2010 iGEM team has developed a standard for the electronic distribution of diagrams, detailed in BBF RFC 68. We also created two new software tools: WikiDust and PartsRobot.

Update 11/30/2010:
This page will be locked soon, so be sure to visit the [http://www.tinkercell.com/plugins/wikidust WikiDust] and [http://sourceforge.net/p/partsrobot/home/ PartsRobot] sites for more current information.

Wikidust banner.png

A Standard for Electronic Diagrams

Standard, unambiguous diagrams are central to communication in many established fields of engineering, but have not yet been widely adopted by synthetic biologists. Through the use of diagrams based on SBOL-visual ([http://bbf.openwetware.org/RFC.html#BBF_RFC_16:_Synthetic_Biology_Open_Language_Visual_.28SBOLv.29_Specification BBF RFC 16]) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. Usefulness of shared diagrams depends both on a standard set of symbols and on the method of distribution. Therefore the two main requirements for our proposed standard, [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_68:_Standard_for_the_Electronic_Distribution_of_SBOLv_Diagrams BBF RFC 68], are:

  1. The use of SBOLv symbols
  2. The linking of symbols to reference entry pages on the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts] using http URLs

In the resulting diagram, the reader can click on portions which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram. This makes research easier and promotes better part descriptions.

Software to Create and Share Standards-Compliant Diagrams

WikiDust is a plugin for TinkerCell, a computer-aided design tool developed here at the [http://www.washington.edu/ University of Washington]. WikiDust can be used to export diagrams of TinkerCell models to the iGEM wiki or other webpages. Our goal in creating WikiDust is to provide an easy way to share models and to encourage iGEM teams and researchers to describe their parts more completely. This, in turn, will help others reuse them in future projects.

Washington rightclick.png
Uw sauro linkpanel.png

One thing WikiDust does is provide a method to associate TinkerCell items, such as promoters or coding sequences, with parts on the Registry. The same mechanism could also be extended in the future to download reaction kinetics and other parameters from sources like the [http://www.ncbi.nlm.nih.gov/pubmed/20160009 Standard Virtual Parts Repository] or the [http://www.ncbi.nlm.nih.gov/pubmed/16381960 Biomodels Database]. For now though, it demonstrates the feasability of using the publicly available [http://www.sbolstandard.org Standard Biological Parts Knowledgebase (SBPkb)] to retrieve part information using Semantic Web standards.

Uw sauro mapprompt.png










To associate a link with an item in TinkerCell, right click on it and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one. Click "Use Selected" to choose one from the list, or enter your own link and click "Use Custom".

After the model of your device or system is finished, and you've added all the links you want, you can upload a diagram of it to a webpage. Just choose "Create Imagemap" from the TinkerCell plugins menu, and change any options you want in the window that pops up. WikiDust will automatically handle uploading to the iGEM wiki, or it can just display code for you to copy and paste to another site. The diagram will be interactive; clicking an item will take you to the correct part page. In fact, our tse2/tsi2 diagram was generated using WikiDust.


To start using WikiDust you’ll need the main TinkerCell program, as well as Python and Subversion. All three can be found on the [http://www.tinkercell.com/downloads-2 TinkerCell download page].


Partsrobot banner.png

Registry Submission Made Easy

PartsRobot is a command-line tool that can submit many parts to the [http://partsregistry.org/Main_Page Registry] at once. This makes it fast and easy to enter information about a series of similar parts—promoters of different strengths, variations on a protein, etc.

Uw sauro spreadsheet.png






















Uw sauro submitter mockup.png

Using PartsRobot is simple. Just fill out the template spreadsheet with information about each part. Then, in a command prompt, type:

python partsrobot.py submit yourspreadsheet.csv

(Exact command varies with OS and file locations. See the README for details.)

Once launched, the program will log into the Registry and check your parts for syntax errors. After you give the go-ahead, it will submit them. Most of our parts were submitted this way.


You can download PartsRobot from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page].

← New Vectors       Overview of Tools We Used →

Retrieved from "http://2010.igem.org/Team:Washington/Tools_Created/New_Software"