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Team:SYSU-Software/Tutorial
From 2012.igem.org
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Tutorial
Contents |
Home
On the left is the logo of
BiArkit which is created by 2012
SYSU-software igem team.
In the main display window, there are
six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA,
Biobrick, and Simulator, which will take you to corresponding parts once
clicking.
Genome Browser
In the main display window, the first
ribbon is the sequence that the user has inputted, and the third ribbon shows
the corresponding gene annotation. You can click any annotation that you want,
and then the sequence site will automatically jump to the fragment related to
it. Between those ribbons is an adjustable slider, which can adjust your view
location by sliding to the left or to the right. Above the sequence are the head
and tail of the location that you are viewing while the head and tail of the
whole sequence are displayed in the bottom textbox. What’s more, the textbox
contains the length, product, tag of the sequence, and links of related papers
are also included sometimes.
On the left, there are two useful tools:
you can search the fragment that you want by position, product or name (Position
represents the position of its head, Product and Name stand for products and
names of related genes, both of them support fuzzy search), besides, whether you
choose product or name, a dialog box that contains names of related genes will
appear; the slider of Zoom is designed for regulating the display frame rate of
the sequence.
Biobrick
Notice that there is a finder on the
left; you can search biobricks by key words and then a window showing the search
result will pop up. Bellow it is a list of biobrick. Turning to the right, a
schematic diagram that shows components of the biobrick is on the top. And
related information about the biobrick is below it.
RiboSwitch
Procedure:
On the right is the main operating area
and you can choose your target type (your experimental object) and corresponding
target name, aptamer and regulation direction. Attention should be paid to the
input box named Input your Target. You can search your target name by key words
or even several letters of it. It should be useful to you. Click
GO and you will see a picture. The
designed riboswitch is in the dotted box on the top left corner. Below it is a
diagram to show how the riboswitch works. Besides, there is a list on the left
box. It records your choices that you have made in created riboswich project,
and you need only click GO next time.
SiRNA
Procedure:
Network Illustrator
Procedure:
In the main display window, you will see
a network from KEGG website. On the left, there is a finder; you can search
elements in the network and a window that shows the search result will pop up.
Bellow it is a box containing a list of files that you have opened. Pay
attention that you can right click the main display window to open another KEGG
xml file or to search any element in the network (choose
find element).
Simulator
Procedure:
There are 5 options for you to select: exhaustive single
deletion, reaction deletion, Fva analysis,
Perturbation analysis and PhPP analysis.
They with FBA solve will be introduced in detail. You can select all of them or
part of them, or even nothing, then click
Go. If you select none of them, you will see a table showed basic
information of each reaction. If you select several of them, the corresponding
windows will tiled in the resulting window. If you select reaction deletion
option, a selection of the reaction you want to wipe off is required, and if
there is any change, it will be highlighted in red font.
1.
FBA_solve
Above column displays names of the
reactions while the right one displays the flux amount of each reaction
2. exanstive single deletion
Calculate the flux amount of the
objective reaction when each other reaction is deleted one by one.
Left column display names of the
reactions
The right one displays the flux amount
of objective reaction the user has chosen, when each other reaction is deleted
one by one.
when rolling down the screen, you can
see the reaction-names related to lethal deletions, sub optimal deletions and
super optimaldeletions.
This graph shows how many lethal
knockouts in each reaction subsystem. The information of the reaction subsystem
can be attained in SBML
This hist graph shows the frequency of
reaction which has different quantified effect showed in the X-axis opon
objective reaction.
3. reaction deletion
Middle column displays the flux amount
of the wild type while the right column displays the mutant type, which is
calculated based on the deletion of one chosen reaction.
4. FVA analysis
5.Perturbation
analysis:
X-axis refers
to the continuously increasing flux value of the chosen reaction.
Y-axis refers
to the flux value of the objective reaction according to the variation of the
flux value of chosen reaction in the X-axis
6.PhPP analysis
The value
marked on the contour represents the flux value of the objective reaction based
on the variation of two chosen reactions The color of the graph changes
according to the altitude, namely, the objective flux value.
G-Circle
Procedure:
Clotho
All above seven parts have been
developed into
Clotho apps and have been updated
into
Clotho, which has met the
requirements for gold medal of IGEM.
Home
Genome Browser
Biobrick
RiboSwitch
SiRNA
Network Illustrator
Simulator
G-Circle
