Team:KULeuven/Tools

From 2008.igem.org

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Under Construction...
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'''DEPRECATED PAGE'''
 +
{{:Team:KULeuven/Tools/Styling}}
 +
{{:Team:KULeuven/Tools/Scripting}}
 +
{{:Team:KULeuven/Tools/Header}}
== Templates ==
== Templates ==
 +
 +
All the useful templates are collected here, each one has a link to the template page and offers some information on the usage of the template. For convenience a clip button is offered to directly copy corresponding code to the clipboard ('''works only in IE, Firefox does not allow direct access to the clipboard!''').
 +
=== General ===
=== General ===
==== [[Team:KULeuven/Tools/Navigation_Bar | Navigation Bar]] ====
==== [[Team:KULeuven/Tools/Navigation_Bar | Navigation Bar]] ====
-
'''Usage:'''
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<html>
-
<nowiki>{{:Team:KULeuven/Tools/Navigation_Bar}}</nowiki>
+
<div class="general"><div>
 +
<center>
 +
<input type="text" class="input" id="styled" name="navigation_bar" value="{{:Team:KULeuven/Tools/Navigation_Bar}}"/>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(navigation_bar)"/>
 +
</center>
 +
<hr>
 +
<p>
 +
The navigation bar used throughout the wiki. The template contains all the CSS and Javascript code inline. The structure itself is given at the bottom and can be modified as desired.
 +
<br>
 +
In general one submenu in the bar is coded as (in this example the Project Section):
 +
<br><br>
 +
<center>
 +
<textarea class="textarea" rows="8">
 +
<!-- PROJECT SECTION -->
 +
<li><a href="https://2008.igem.org/Team:KULeuven/Project"
 +
onmouseover="mopen('m4')" onmouseout="mclosetime()">The Project</a>
 +
<div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 +
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
 +
<a href="https://2008.igem.org/Team:KULeuven/Concreties">Concrete Ideas</a>
 +
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
 +
</div>
 +
 
 +
</li>
 +
</textarea>
 +
</center>
 +
Important: change the 'm4' to the appropriate value, e.g. if there are already 7 submenu's present it should be 'm8'.
 +
</p>
 +
<p>
 +
If the submenu contains no entries (single link, no dropdown behaviour, e.g. Home, Modeling) you can make use of the "nomenu" class, this way the menu item does not change color in hover mode (mouse located on the menu item). Simply add <em>class="nomenu"</em> between <em>a</em> and <em>href</em>.
 +
</p>
 +
<p>
 +
The code of the old navigation bar (no dropdown):
 +
<br><br>
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{|style="border-spacing:6px; text-align:center; color:white" width="960px"</dd>
 +
|-bgcolor="#003E81" padding="3"
 +
![[Team:KULeuven|Home]]
 +
![[Team:KULeuven/Team|The Team]]
 +
![[Team:KULeuven/Road Map|Road Map]]
 +
![[Team:KULeuven/Project|The Project]]
 +
![[Team:KULeuven/Parts|Parts Submitted to the Registry]]
 +
![[Team:KULeuven/Modeling|Modeling]]
 +
![[Team:KULeuven/Notebook|Notebook]]
 +
|}
 +
</textarea>
 +
</center>
 +
</p>
 +
</div></div>
 +
</html>
 +
 
 +
==== [[Team:KULeuven/Tools/New_Day | New Day]] ====
 +
 
 +
<html>
 +
<div class="general"><div>
 +
<p>The day template that is preloaded into a notebook day. The result can be seen in the [[Team:KULeuven/Notebook |Notebook]] section, when you click on an unmodified day, you'll get the edit screen, prefilled with the contents of the New_Day template. To create a calendar using this template use the code:
 +
</p>
 +
<center>
 +
<input type"text" class="input" id="styled" name="day_template" value="{{#calendar: query=preload=:Team:Kuleuven/Tools/New_Day}}"/>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(day_template)"/>
 +
</center>
 +
<p>
 +
The template adds a date retriever, displaying links such as yesterday, tomorrow, ..., to ease the navigation for the user. The javascript is found <a href="https://2008.igem.org/Team:KULeuven/Tools/New_Day/Date_Retriever">here</a>.
 +
</p>
 +
</div></div>
 +
</html>
=== Lab Templates ===
=== Lab Templates ===
-
==== [[Team:KULeuven/Tools/PCR | PCR sheet]] ====
 
-
'''Usage:'''
+
'''All lab templates below are heavily inspired by the [https://2007.igem.org/Paris iGEM Paris 2007 team], and were merely reconstructed by the KULeuven iGEM team. We owe great thanks to them.'''
-
<nowiki>{{:Team:KULeuven/Tools/PCR
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-
|tanneal=55
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-
|telong=2'30"
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-
|ncycles=30
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-
|buffer=5x 10μL
+
-
|mgcl=10μM 0μL
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-
|dntp=10μM 1μL
+
-
|fwprimername=6 LacZ-Fw
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-
|fwprimerconc=10μM 2.5μL
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-
|rvprimername=7 LacZ-Rv
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-
|rvprimerconc=10μM 2.5μL
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-
|water=34μL
+
-
|polymerase=Taq 0.5μL
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|dna=0.5μL of E. coli DNA extract
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-
|size=952bp
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-
|success=YES/NO
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-
|image=pcrproducts_GE.jpg
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-
|lane=3+4
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-
}}</nowiki>
+
-
'''Result:'''
+
==== [[Team:KULeuven/Tools/PCR | PCR sheet]] ====
 +
<html>
 +
<div class="general"><div>
 +
<center>
 +
<textarea class="textarea" id="styled" name="PCR" rows="10">
 +
{{:Team:KULeuven/Tools/PCR
 +
|tanneal=
 +
|telong=
 +
|ncycles=
 +
|buffer=
 +
|mgcl=
 +
|dntp=
 +
|fwprimername=
 +
|fwprimerconc=
 +
|rvprimername=
 +
|rvprimerconc=
 +
|water=
 +
|polymerase=
 +
|dna=
 +
|size=
 +
|success=
 +
|image=
 +
|lane=
 +
}}
 +
</textarea>
 +
<br>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(PCR)"/>
 +
</center>
 +
</div></div>
 +
<div class="example"><div>
 +
<strong>Example</strong> (result below)
 +
<center>
 +
<textarea class="textarea" rows="10">
{{:Team:KULeuven/Tools/PCR
{{:Team:KULeuven/Tools/PCR
|tanneal=55
|tanneal=55
Line 53: Line 136:
|lane=3+4
|lane=3+4
}}
}}
 +
</textarea>
 +
</center>
 +
</div></div>
 +
</html>
 +
<br>
 +
{{:Team:KULeuven/Tools/PCR
 +
|tanneal=55
 +
|telong=2'30"
 +
|ncycles=30
 +
|buffer=5x 10μL
 +
|mgcl=10μM 0μL
 +
|dntp=10μM 1μL
 +
|fwprimername=6 LacZ-Fw
 +
|fwprimerconc=10μM 2.5μL
 +
|rvprimername=7 LacZ-Rv
 +
|rvprimerconc=10μM 2.5μL
 +
|water=34μL
 +
|polymerase=Taq 0.5μL
 +
|dna=0.5μL of E. coli DNA extract
 +
|size=952bp
 +
|success=YES/NO
 +
|image=pcrproducts_GE.jpg
 +
|lane=3+4
 +
}}
 +
----
==== [[Team:KULeuven/Tools/Digestion | Digestion sheet]] ====
==== [[Team:KULeuven/Tools/Digestion | Digestion sheet]] ====
-
'''Usage:'''
+
<html>
-
<nowiki>
+
<div class="general"><div>
-
{{:Team:KULeuven/Tools/Digestion
+
<center>
-
|nr=D12
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<textarea class="textarea" id="styled" name="digestion" rows="10">
-
|product=Cre ORF
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{{:Team:KULeuven/Tools/Digestion
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|matrix=pJ61047
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|nr=
-
|enz1=Pst1
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|product=
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|enz2=Xba1
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|matrix=
-
|size=1063bp
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|enz1=
-
|desc=Cre ORF extracted for further usage
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|enz2=
-
}}
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|size=
-
</nowiki>
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|desc=
 +
}}
 +
</textarea>
 +
<br>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(digestion)"/>
 +
</center>
 +
</div></div>
 +
<div class="example"><div>
 +
<strong>Example</strong> (result below)
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{{:Team:KULeuven/Tools/Digestion
 +
|nr=D12
 +
|product=Cre ORF
 +
|matrix=pJ61047
 +
|enz1=Pst1
 +
|enz2=Xba1
 +
|size=1063bp
 +
|desc=Cre ORF extracted for further usage
 +
}}
 +
</textarea>
 +
</center>
 +
</div></div>
 +
</html>
 +
<br>
-
'''Result:'''
 
{{:Team:KULeuven/Tools/Digestion
{{:Team:KULeuven/Tools/Digestion
|nr=D12
|nr=D12
Line 79: Line 210:
|desc=Cre ORF extracted for further usage
|desc=Cre ORF extracted for further usage
}}
}}
-
 
+
----
==== [[Team:KULeuven/Tools/Ligation | Ligation sheet]] ====
==== [[Team:KULeuven/Tools/Ligation | Ligation sheet]] ====
-
'''Usage:'''
+
<html>
 +
<div class="general"><div>
 +
<center>
 +
<textarea class="textarea" id="styled" name="ligation" rows="10">
 +
{{:Team:KULeuven/Tools/Ligation
 +
|nr=
 +
|insert=
 +
|insert_vol=
 +
|vector=
 +
|vector_vol=
 +
|comm=
 +
|ncol=
 +
}}
 +
</textarea>
 +
<br>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(ligation)"/>
 +
</center>
 +
</div></div>
 +
<div class="example"><div>
 +
<strong>Example</strong> (result below)
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{{:Team:KULeuven/Tools/Ligation
 +
|nr=L21
 +
|insert=D12 Cre ORF
 +
|insert_vol=6µL
 +
|vector=D1 pJ23100
 +
|vector_vol=2µL
 +
|comm=construction of BioBrick: Cre-recombinase under control of strong promotor
 +
|ncol=30
 +
}}
 +
</textarea>
 +
</center>
 +
</div></div>
 +
</html>
 +
<br>
 +
 
 +
{{:Team:KULeuven/Tools/Ligation
 +
|nr=L21
 +
|insert=D12 Cre ORF
 +
|insert_vol=6µL
 +
|vector=D1 pJ23100
 +
|vector_vol=2µL
 +
|comm=construction of BioBrick: Cre-recombinase under control of strong promotor
 +
|ncol=30
 +
}}
 +
----
 +
==== [[Team:KULeuven/Tools/96-well | 96-Well Plate]] ====
 +
 
 +
<html>
 +
<div class="general"><div>
 +
<center>
 +
<textarea class="textarea" id="styled" name="wells96" rows="10">
 +
{{:Team:KULeuven/Tools/96-well
 +
|title=
 +
|A1=
 +
|A2=
 +
|A3=
 +
|A4=
 +
|A5=
 +
|A6=
 +
|A7=
 +
...
 +
|B1=
 +
|C1=
 +
|D1=
 +
|E1=
 +
|F1=
 +
...
 +
}}
 +
</textarea>
 +
<br>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(wells96)"/>
 +
</center>
 +
<hr>
 +
The 96 wells sheet extends from 1-12 horizontally, and from A-H vertically, not all squares have been given in the code above, but are easily added.
 +
</div></div>
 +
<div class="example"><div>
 +
<strong>Example</strong> (result below)
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{{:Team:KULeuven/Tools/96-well
 +
|title=Induced Response
 +
|A1=LB + 0µM IPTG
 +
|A2=LB + 0µM IPTG
 +
|A3=LB + 5µM IPTG
 +
|A4=LB + 5µM IPTG
 +
|A5=LB + 10µM IPTG
 +
|A6=LB + 10µM IPTG
 +
|A7=etc
 +
|B1=LB 2 + 0µM IPTG
 +
|C1=LB 3 + 0µM IPTG
 +
|D1=LB 4 + 0µM IPTG
 +
|E1=LB 5 + 0µM IPTG
 +
|F1=etc
 +
}}
 +
</textarea>
 +
</center>
 +
</div></div>
 +
</html>
 +
<br>
 +
 
 +
{{:Team:KULeuven/Tools/96-well
 +
|title=Induced Response
 +
|A1=LB + 0µM IPTG
 +
|A2=LB + 0µM IPTG
 +
|A3=LB + 5µM IPTG
 +
|A4=LB + 5µM IPTG
 +
|A5=LB + 10µM IPTG
 +
|A6=LB + 10µM IPTG
 +
|A7=etc
 +
|B1=LB 2 + 0µM IPTG
 +
|C1=LB 3 + 0µM IPTG
 +
|D1=LB 4 + 0µM IPTG
 +
|E1=LB 5 + 0µM IPTG
 +
|F1=etc
 +
}}
 +
 
 +
=== Collection Templates ===
 +
==== [[Team:KULeuven/Tools/Oligo | Primer Collection]] ====
 +
 
 +
<html>
 +
<div class="general"><div>
 +
<center>
 +
<textarea class="textarea" id="styled" name="oligo" rows="6">{{:Team:KULeuven/Tools/Oligo
 +
|nr=
 +
|name=
 +
|sequence=
 +
|Tm=
 +
|length=
 +
|comments=
 +
}}
 +
</textarea>
 +
<br>
 +
<input type="button" class="button" id="clip" value="Clip" onClick="clipboard(oligo)"/>
 +
</center>
 +
<hr>
 +
To start the primer collection page, copy following code into the edit screen:
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{|cellspacing="1" width=100%
 +
! style="background:#003E81; color: white" colspan="5" | Table of Oligos
 +
|-style="background:#99CCFF" align="center"
 +
| width=5% | Number
 +
| width=10% | Name
 +
| width=55% | Sequence
 +
| width=5% | Tm (°C)
 +
| width=5% | Length
 +
| width=20% | Comments
 +
...
 +
|}
 +
</textarea>
 +
</center>
 +
Where you see the dots the template codelines will be added to. The dots will be replaced by the primer templates sequentially:
 +
<br>
 +
{{:Team:KULeuven/Tools/Oligo ...}}
 +
<br>
 +
{{:Team:KULeuven/Tools/Oligo ...}}
 +
</div></div>
 +
<div class="example"><div>
 +
<strong>Example</strong> (result below)
 +
<center>
 +
<textarea class="textarea" rows="10">
 +
{|cellspacing="1" width=100%
 +
! style="background:#003E81; color: white" colspan="5" | Table of Oligos
 +
|-style="background:#99CCFF" align="center"
 +
| width=5% | Number
 +
| width=10% | Name
 +
| width=55% | Sequence
 +
| width=5% | Tm (°C)
 +
| width=5% | Length
 +
| width=20% | Comments
 +
{{:Team:KULeuven/Tools/Oligo}}
 +
{{:Team:KULeuven/Tools/Oligo}}
 +
|}
 +
</textarea>
 +
</center>
 +
</div></div>
 +
</html>
 +
<br>
 +
 
 +
{|cellspacing="1" width=100%
 +
! style="background:#003E81; color: white" colspan="5" | Table of Oligos
 +
|-style="background:#99CCFF" align="center"
 +
| width=5% | Number
 +
| width=10% | Name
 +
| width=55% | Sequence
 +
| width=5% | Tm (°C)
 +
| width=5% | Length
 +
| width=20% | Comments
 +
{{:Team:KULeuven/Tools/Oligo}}
 +
{{:Team:KULeuven/Tools/Oligo}}
 +
|}
 +
----
 +
 
 +
==== [[Team:KULeuven/Tools/Freezer | Freezer]] ====
 +
 
 +
<html>
 +
<div class="general"><div>
 +
All the information to start the Freezer page and making use of the Freezer templates is on the <a href="https://2008.igem.org/Team:KULeuven/Tools/Freezer">Freezer Tools</a> page.
 +
</div></div>
 +
</html>
 +
 
 +
== CSS ==
 +
=== [[User:Avdmeers/SimpleCalendar.css | Calendar CSS file]] ===
-
==CSS==
+
== Javascript ==
-
==== [[User:Avdmeers/SimpleCalendar.css | Calendar CSS file]] ====
+

Latest revision as of 10:30, 29 October 2008

DEPRECATED PAGE

  dock/undock dropdown  

Contents

Templates

All the useful templates are collected here, each one has a link to the template page and offers some information on the usage of the template. For convenience a clip button is offered to directly copy corresponding code to the clipboard (works only in IE, Firefox does not allow direct access to the clipboard!).

General

Navigation Bar

The navigation bar used throughout the wiki. The template contains all the CSS and Javascript code inline. The structure itself is given at the bottom and can be modified as desired.
In general one submenu in the bar is coded as (in this example the Project Section):

Important: change the 'm4' to the appropriate value, e.g. if there are already 7 submenu's present it should be 'm8'.

If the submenu contains no entries (single link, no dropdown behaviour, e.g. Home, Modeling) you can make use of the "nomenu" class, this way the menu item does not change color in hover mode (mouse located on the menu item). Simply add class="nomenu" between a and href.

The code of the old navigation bar (no dropdown):

New Day

The day template that is preloaded into a notebook day. The result can be seen in the [[Team:KULeuven/Notebook |Notebook]] section, when you click on an unmodified day, you'll get the edit screen, prefilled with the contents of the New_Day template. To create a calendar using this template use the code:

The template adds a date retriever, displaying links such as yesterday, tomorrow, ..., to ease the navigation for the user. The javascript is found here.

Lab Templates

All lab templates below are heavily inspired by the iGEM Paris 2007 team, and were merely reconstructed by the KULeuven iGEM team. We owe great thanks to them.

PCR sheet


Example (result below)

PCR:
PCR Settings
Annealing (°C)
55°
Time Elongation
2'30"
Number of Cycles
30
Buffer (5x) 5x 10μL
MgCl2 10 µM 10μM 0μL
dNTP 10 µM 10μM 1μL
Oligo F 10 µM 6 LacZ-Fw 10μM 2.5μL
Oligo R 10 µM 7 LacZ-Rv 10μM 2.5μL
Water 34μL
Polymerase Taq 0.5μL
DNA 0.5μL of E. coli DNA extract
Expected Size
952bp
Success
YES/NO
Image (click to enlarge)
30px
Lane (0=ladder)
3+4

Digestion sheet


Example (result below)

Digestion Products
Number Product Name Matrix Name Enzyme 1 Enzyme 2 Size Description
D12 Cre ORF pJ61047 XbaI PstI 1063bp Cre ORF extracted for further usage

Ligation sheet


Example (result below)

Ligations
Number Insert Insert Volume (µL) Vector Vector Volume (µL) Comments Number of colonies
L21 D12 Cre ORF 6µL D1 pJ23100 2µL construction of BioBrick: Cre-recombinase under control of strong promotor 30

96-Well Plate


The 96 wells sheet extends from 1-12 horizontally, and from A-H vertically, not all squares have been given in the code above, but are easily added.
Example (result below)

96-Well Plate: Induced Response
1 2 3 4 5 6 7 8 9 10 11 12
A LB + 0µM IPTGLB + 0µM IPTGLB + 5µM IPTG LB + 5µM IPTGLB + 10µM IPTGLB + 10µM IPTG etc// ///
B LB 2 + 0µM IPTG// /// /// ///
C LB 3 + 0µM IPTG// /// /// ///
D LB 4 + 0µM IPTG// /// /// ///
E LB 5 + 0µM IPTG// /// /// ///
F etc// /// /// ///
G /// /// /// ///
H /// /// /// ///

Collection Templates

Primer Collection


To start the primer collection page, copy following code into the edit screen:
Where you see the dots the template codelines will be added to. The dots will be replaced by the primer templates sequentially:
{{:Team:KULeuven/Tools/Oligo ...}}
{{:Team:KULeuven/Tools/Oligo ...}}
Example (result below)

Table of Oligos
Number Name Sequence Tm (°C) Length Comments
{{{nr}}} {{{name}}} {{{sequence}}} {{{length}}} {{{Tm}}} {{{comments}}}
{{{nr}}} {{{name}}} {{{sequence}}} {{{length}}} {{{Tm}}} {{{comments}}}

Freezer

All the information to start the Freezer page and making use of the Freezer templates is on the Freezer Tools page.

CSS

Calendar CSS file

Javascript

Retrieved from "http://2008.igem.org/Team:KULeuven/Tools"