Revision as of 13:51, 15 August 2014

USTC-Software | Welcome

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Description

Ailuropoda is a data visualizational open source software specially designed for biologists, which can be used to show gene regulation and metabolic network. When a node is selected, our software can quickly form a net with the nodes close to it. When a gene sequence is provided, such as a BioBrick part, our software can use homology method to predict the impact it gives on the gene regulatory network. Furthermore, the software provides users with various interfaces so that the entire network, or a part of it, can be exported into corresponding format which can be imported into other professional softwares for network analysis.On this platform, users can create, modify and complete different biological networks based on the information they get from online collaboration.

Next we will introduce specific functions of our software.

Functions Already Realized:

Display of the Relationship

When the user inputs the information of a node, the software will show the three-decker network associated with the node. Other nodes will be arranged according to the strength of their relationship with the central node, and highlighted by varied colors as well. The user can also input two or more nodes to find their relationship. Our software will show all the paths connecting them that satisfy the distance the user sets. Moreover, every node and arc in the network is attached with an extensive literature, the newest included, and the user can read the literature along all the paths to study the various relationship in the network more expressly.

Functions to Be Realized:

Providing All Kinds of Interfaces and Network Analysis

The user can select the entire network (or a part of it), export it into appropriate format, and then import the file into some professional biological software for function analysis, such as SimBiology in Matlab. Moreover, our software provides APIs, enabling users to write some small plug-ins themselves to realize user-defined functions.

Collaborative Networking and Multi-field Information Exchange

One biologist can only build a small part of network, which is already hard work. However, they can make use of the platform our software provides to upload their achievements and our software will integrate these networks. Biologists from different fields can exchange all kinds of information, therefore they may discover enlightening links among various research projects, which can guide them to a better decision on their further research. It will also effectively enhance the development of varied fields of biology. An example of this is that molecular biologists can point out metabolic pathways for synthetic biologists, and synthetic biologists design and optimize product circuits using BioBrick parts for molecular biologists.

Prospective:

Ailuropoda is currently based on the data of E.coli K-12, and we will continue to enrich our data with the help of users. With an enriched database, the software will be of great value and wide application.

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-         <p style="font-size:32px">iGEM meets USTC-Software</p>
+         <p style="font-size:32px">Description</p>
          <div class="underline-large"></div>
        </div>
-      <div class="row large-12 columns large-centered">
+     <div class="row large-12 columns large-centered">
-        <h3>Why?</h3>
+<p class="p0">
-        <div class="underline-small"></div>
+	Ailuropoda&nbsp;is&nbsp;a&nbsp;data&nbsp;visualizational&nbsp;open&nbsp;source&nbsp;software&nbsp;specially&nbsp;designed&nbsp;for&nbsp;biologists,&nbsp;which&nbsp;can&nbsp;be&nbsp;used&nbsp;to&nbsp;show&nbsp;gene&nbsp;regulation&nbsp;and&nbsp;metabolic&nbsp;network.&nbsp;When&nbsp;a&nbsp;node&nbsp;is&nbsp;selected,&nbsp;our&nbsp;software&nbsp;can&nbsp;quickly&nbsp;form&nbsp;a&nbsp;net&nbsp;with&nbsp;the&nbsp;nodes&nbsp;close&nbsp;to&nbsp;it.&nbsp;When&nbsp;a&nbsp;gene&nbsp;sequence&nbsp;is&nbsp;provided,&nbsp;such&nbsp;as&nbsp;a&nbsp;BioBrick&nbsp;part,&nbsp;our&nbsp;software&nbsp;can&nbsp;use&nbsp;homology&nbsp;method&nbsp;to&nbsp;predict&nbsp;the&nbsp;impact&nbsp;it&nbsp;gives&nbsp;on&nbsp;the&nbsp;gene&nbsp;regulatory&nbsp;network.&nbsp;Furthermore,&nbsp;the&nbsp;software&nbsp;provides&nbsp;users&nbsp;with&nbsp;various&nbsp;interfaces&nbsp;so&nbsp;that&nbsp;the&nbsp;entire&nbsp;network,&nbsp;or&nbsp;a&nbsp;part&nbsp;of&nbsp;it,&nbsp;can&nbsp;be&nbsp;exported&nbsp;into&nbsp;corresponding&nbsp;format&nbsp;which&nbsp;can&nbsp;be&nbsp;imported&nbsp;into&nbsp;other&nbsp;professional&nbsp;softwares&nbsp;for&nbsp;network&nbsp;analysis.On&nbsp;this&nbsp;platform,&nbsp;users&nbsp;can&nbsp;create,&nbsp;modify&nbsp;and&nbsp;complete&nbsp;different&nbsp;biological&nbsp;networks&nbsp;based&nbsp;on&nbsp;the&nbsp;information&nbsp;they&nbsp;get&nbsp;from&nbsp;online&nbsp;collaboration.&nbsp;
-        <p>The USTC Software team will organize a worldwide team meet up on August 15th, which will be held at University of Science and Technology of China and planed to last about three days. This meeting is mainly for software tracks. Because most of the meet-ups are among wet tracks, the meeting could be a great opportunity to enhance communication between software teams. Teams will present a brief overview of their project along with their specific summer goals, then discuss alternative ways to approach their projects, and end the meeting with brainstorming ways for the teams to collaborate on either coding or human practices. !
+</p>
-        </p>
+<p class="p0">
-      </div>
+	Next&nbsp;we&nbsp;will&nbsp;introduce&nbsp;specific&nbsp;functions&nbsp;of&nbsp;our&nbsp;software.
-      <div class="row">
+</p>
-        <div class="large-6 columns">
+<h1>
-          <h3>When?</h3>
+	Functions&nbsp;Already&nbsp;Realized:
-          <div class="underline-small"></div>
+</h1>
-          <p>August 15 - August 17, 2014</p>
+<h2>
-        </div>
+	Display&nbsp;of&nbsp;the&nbsp;Relationship
+</h2>
-        <div class="large-6 columns">
+<p class="p0">
-          <h3>Where?</h3>
+	When&nbsp;the&nbsp;user&nbsp;inputs&nbsp;the&nbsp;information&nbsp;of&nbsp;a&nbsp;node,&nbsp;the&nbsp;software&nbsp;will&nbsp;show&nbsp;the&nbsp;three-decker&nbsp;network&nbsp;associated&nbsp;with&nbsp;the&nbsp;node.&nbsp;Other&nbsp;nodes&nbsp;will&nbsp;be&nbsp;arranged&nbsp;according&nbsp;to&nbsp;the&nbsp;strength&nbsp;of&nbsp;their&nbsp;relationship&nbsp;with&nbsp;the&nbsp;central&nbsp;node,&nbsp;and&nbsp;highlighted&nbsp;by&nbsp;varied&nbsp;colors&nbsp;as&nbsp;well.&nbsp;The&nbsp;user&nbsp;can&nbsp;also&nbsp;input&nbsp;two&nbsp;or&nbsp;more&nbsp;nodes&nbsp;to&nbsp;find&nbsp;their&nbsp;relationship.&nbsp;Our&nbsp;software&nbsp;will&nbsp;show&nbsp;all&nbsp;the&nbsp;paths&nbsp;connecting&nbsp;them&nbsp;that&nbsp;satisfy&nbsp;the&nbsp;distance&nbsp;the&nbsp;user&nbsp;sets.&nbsp;Moreover,&nbsp;every&nbsp;node&nbsp;and&nbsp;arc&nbsp;in&nbsp;the&nbsp;network&nbsp;is&nbsp;attached&nbsp;with&nbsp;an&nbsp;extensive&nbsp;literature,&nbsp;the&nbsp;newest&nbsp;included,&nbsp;and&nbsp;the&nbsp;user&nbsp;can&nbsp;read&nbsp;the&nbsp;literature&nbsp;along&nbsp;all&nbsp;the&nbsp;paths&nbsp;to&nbsp;study&nbsp;the&nbsp;various&nbsp;relationship&nbsp;in&nbsp;the&nbsp;network&nbsp;more&nbsp;expressly.
-          <div class="underline-small"></div>
+</p>
-          <ul>
+<h1>
-            <li>University of Science and Technology of China</li>
+	Functions&nbsp;to&nbsp;Be&nbsp;Realized:
-             <li>USTC-Software</li>
+</h1>
-           </ul>
+<h2>
-        </div>
+	Providing&nbsp;All&nbsp;Kinds&nbsp;of&nbsp;Interfaces&nbsp;and&nbsp;Network&nbsp;Analysis
+</h2>
+<p class="p0">
-      </div>
+	The&nbsp;user&nbsp;can&nbsp;select&nbsp;the&nbsp;entire&nbsp;network&nbsp;(or&nbsp;a&nbsp;part&nbsp;of&nbsp;it),&nbsp;export&nbsp;it&nbsp;into&nbsp;appropriate&nbsp;format,&nbsp;and&nbsp;then&nbsp;import&nbsp;the&nbsp;file&nbsp;into&nbsp;some&nbsp;professional&nbsp;biological&nbsp;software&nbsp;for&nbsp;function&nbsp;analysis,&nbsp;such&nbsp;as&nbsp;SimBiology&nbsp;in&nbsp;Matlab.&nbsp;Moreover,&nbsp;our&nbsp;software&nbsp;provides&nbsp;APIs,&nbsp;enabling&nbsp;users&nbsp;to&nbsp;write&nbsp;some&nbsp;small&nbsp;plug-ins&nbsp;themselves&nbsp;to&nbsp;realize&nbsp;user-defined&nbsp;functions.
-      <div class="row">
+</p>
-      <div class="large-12 columns large-centered">
+<h2>
-          <h3>Who?</h3>
+	Collaborative&nbsp;Networking&nbsp;and&nbsp;Multi-field&nbsp;Information&nbsp;Exchange
-          <div class="underline-small"></div>
+</h2>
-           <p>Members from iGEM teams will attend our meetup </p>
+<p class="p0">
-      </div>
+	One&nbsp;biologist&nbsp;can&nbsp;only&nbsp;build&nbsp;a&nbsp;small&nbsp;part&nbsp;of&nbsp;network,&nbsp;which&nbsp;is&nbsp;already&nbsp;hard&nbsp;work.&nbsp;However,&nbsp;they&nbsp;can&nbsp;make&nbsp;use&nbsp;of&nbsp;the&nbsp;platform&nbsp;our&nbsp;software&nbsp;provides&nbsp;to&nbsp;upload&nbsp;their&nbsp;achievements&nbsp;and&nbsp;our&nbsp;software&nbsp;will&nbsp;integrate&nbsp;these&nbsp;networks.&nbsp;Biologists&nbsp;from&nbsp;different&nbsp;fields&nbsp;can&nbsp;exchange&nbsp;all&nbsp;kinds&nbsp;of&nbsp;information,&nbsp;therefore&nbsp;they&nbsp;may&nbsp;discover&nbsp;enlightening&nbsp;links&nbsp;among&nbsp;various&nbsp;research&nbsp;projects,&nbsp;which&nbsp;can&nbsp;guide&nbsp;them&nbsp;to&nbsp;a&nbsp;better&nbsp;decision&nbsp;on&nbsp;their&nbsp;further&nbsp;research.&nbsp;It&nbsp;will&nbsp;also&nbsp;effectively&nbsp;enhance&nbsp;the&nbsp;development&nbsp;of&nbsp;varied&nbsp;fields&nbsp;of&nbsp;biology.&nbsp;An&nbsp;example&nbsp;of&nbsp;this&nbsp;is&nbsp;that&nbsp;molecular&nbsp;biologists&nbsp;can&nbsp;point&nbsp;out&nbsp;metabolic&nbsp;pathways&nbsp;for&nbsp;synthetic&nbsp;biologists,&nbsp;and&nbsp;synthetic&nbsp;biologists&nbsp;design&nbsp;and&nbsp;optimize&nbsp;product&nbsp;circuits&nbsp;using&nbsp;BioBrick&nbsp;parts&nbsp;for&nbsp;molecular&nbsp;biologists.
-      </div>
+</p>
+<h1>
+	Prospective:
+</h1>
+<p class="p0">
+	Ailuropoda&nbsp;is&nbsp;currently&nbsp;based&nbsp;on&nbsp;the&nbsp;data&nbsp;of&nbsp;E.coli&nbsp;K-12,&nbsp;and&nbsp;we&nbsp;will&nbsp;continue&nbsp;to&nbsp;enrich&nbsp;our&nbsp;data&nbsp;with&nbsp;the&nbsp;help&nbsp;of&nbsp;users.&nbsp;With&nbsp;an&nbsp;enriched&nbsp;database,&nbsp;the&nbsp;software&nbsp;will&nbsp;be&nbsp;of&nbsp;great&nbsp;value&nbsp;and&nbsp;wide&nbsp;application.
+</p>
+     </div>
      </div>

Team:USTC-Software

From 2014.igem.org