User Manual
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1. 2 Regulatee This text field is for you to enter the regulatee name A Label named Regulatee is on its above side 3 Regulator Table The left table of the page It includes all the regulators in Operon Operon database 4 Regulatee Table The right table of the page It includes all the regulatees in Operon Operon database 5 Regulator Candidates Table The table below the regulatee name text field If regulatee name is not null this table will contain all the related regulators of this certain regulatee 6 Regulatee Candidates Table The table below the regulator name text field If regulatee name is not null thie table will contain all the related regulatees of this certain regulator 7 Search Button The button with an Icon of iGEM logo If the regulator name and regulatee name are not null you can press this button to generate regulatory relation between the regulator and the regulatee 4 2 Entering Regulator Name There are two ways for you to enter the regulator name 1 Enter the regulator name in the regulator name text field 2 Choose your regulator from regulator table or regulator candidates table In the demo I take the second choice the following picture is what you will get if you click on Operon ada alkB The regulatee candidates of ada alkB will appear in the regulatee candidates table in the meantime Figure 3 Search Regula2. Source Code As Regulon Lib is an open source program its source code can be viewed on github You can download all the source codes in this github repository http github com kfrancischen src Some of the classes are trivial and should not be included in your project if you want to rebuild Regulon Lib These are some brief introductions for the classes e main_GUI class for the welcome page e Search_Page class for the search page e Operon_Operon class for Mode 1 e Gene_Promoter class for Mode 2 e LinkLabel class extended from JLabel using for a specific label All these classes are packed in USTC_Clotho_App package The private variables are always at the bottom of the codes All the source codes and this user manual are written by Francis Chen The images are made by Physics Xu They are members of the 2012 GEM USTC Software Team If you have problems please contact me kfrancischenOgmail com 6 Copyrights amp Acknowledgements 6 1 Database The Operon Operon database and the Gene Promoter database are generated based on database from Regulon DB http regulondb ccg unam mx If you want to use this database please read User Licence first 6 2 Copyrights This clotho app is developed by 2012 iGEM USTC Software Team The copyright is reserved to this team 6 3 Acknowledgements This year our project is sponsored mainly by Life Science Department We also acknowledge our gratitude to SCGY Schoo
3. nemR choice 2588 0 2 gadE mdtEF Biobrick 1 zntAp narP ae Biobrick 2 glgBp nemR ee 4 choice 2589 peron 1 gadE m Biobrick 1 zntAp narP Biobrick 2 insKp nemR choice 2590 Biobrick 1 zntAp nemR Biobrick 2 fumCp narP choice 2591 Biobrick 1 zntAp nemR Biobrick 2 glgBp narP choice 2592 Biobrick 1 zntAp nemR Biobrick 2 insKp narP Figure Using Mode 1 Figure Using Mode 2 4 Searching For Regulons Function for this page e Finding relations between the regulator and regulatee you will use in your experiments e Finding proper regulator candidates if you have regulatee but cannot figure out which regulator to use e Finding proper regulatee candidates if you have regulator but cannot figure out which regulatee to use 4 1 Launching Search Page Click Search on the menu bar in the main page and choose one search page as you like In this section I will take Search In Operon Operon for example The screen shot is pasted below A Ri _ Regulate Lib 5 Sii me A NS aN N e o 1 A os 7 y NO two aly by CBA Regulatees y Regulators j j i Pi E t i Figure 2 Searching Page These are the meanings of each components in search page 1 Regulator This text field is for you to enter the regulator name A Label named Regulator is on its above side
4. Regulen Lib Regulon Lib User Manual 2012 iGEM USTC Software Team 09 2012 Contents 1 Introduction 1 1 Introduction to 2012 iGEM USTC Software Team 1 2 Introduction to Regulon Lib EA A E ES a T22 A RA Beginning Your First Launch Searching For GRN Candidates al Example GRN 2 2 4 4 4 4 6 6 6 5 da dd dd Ove LOW LO LOAD aa e AA AAA ES A Oe E 3 3 How To Generate Results 0 2 02 o Searching For Regulons 4 1 Launching Search Page 0 000000 2 eee 4 2 Entering Regulator Name 0 000005 ee 4 3 Entering Regulatee Name 2 202 050 0004 4 4 Generating Regulatory Relation View Source Code Copyrights amp Acknowledgements Ol Database tiles Ree ee oo EE eS A eee O52 COPY GISNtS 2 e Lo nd e He EE a a ee OR os a ee de 6 3 Acknowledgements 20 e a 4 4 a hte w hole a ad eee S 1 Introduction 1 1 Introduction to 2012 GEM USTC Software Team The 2012 GEM USTC software Team is made up of 9 students from different departments and with different backgrounds Team members are Jack Kang Francis Chen Jaxyon Physics Xu Kaishuar Yang Qi Hu Litong Jiang Yunlong Zheng and Wenjuan Zhang This summer USTC Software Team enjoy having fun together and facing challenges together Our team s main project is concerned with reverse engineering which is a hot topic in synthetic biology Based on this
5. e and negative regulation e 2 unknown regulation The following sections will tell you more specific usage of Regulon Lib 2 Beginning Your First Launch Our app can be built on all the Java IDEs In this user manual I take MyEclipse 10 0 for example The source code can be downloaded from my github repository When first launching our app you ll see this main page File Search Help About Pn ize regulator 2 regulator 3 regulator 4 regulator 5 regulator 6 7 2 tniy Ss Mo i3 regulator 1 Figure 1 Main Page There is one text field at the top of the table Users should first input their matrix size in the text field and then click on button Confirm to commit The main table in the middle is for users to input their regulatory matrix Below the main table two buttons named Mode 1 and Mode 2 are on your choice Mode 1 basically uses Operon Operon database to find the proper results and Mode 2 uses Gene Promoter database Ieee View Source Code section 3 Searching For GRN Candidates The function of the main page is for users to search for Genetic Regulatory Network Candidates in the situation that they lack enough information about the nodes in their GRN In this section an simple example will be shown to you about how to use our database to complete your GRN 3 1 Example GRN The picture below shows an example regulatory network with abstract nodes A and B As for thei
6. idea from August our team began to write this clotho app as an aiding tool For more information about 2012 iGEM USTC Software Team please search in our wiki page http 2012 igem org Team USTC Software For more information about USTC please visit this website http www ustc edu cn 1 2 Introduction to Regulon Lib 1 2 1 Functions Regulon lib is an clotho app written by 2012 iGEM USTC Software Team based on java platform This app includes following functions e Searching for proper regulators and regulatees in databases to complete user s GRN e Searching for regulatory relation in databases 1 2 2 Database In this app the following databases are used e Operon Operon Regulatory Matrix To be specific in this matrix regulators and regulatees are operons The regulatory direction is from the operons in the rows to the operons in corresponding columns Each element of the matrix is their regultion type which is a number chosen from 1 0 1 2 or 2 e Gene Promoter Regulatory Matrix To be specific in this matrix regulators are genes and regulatees are promoters The regulatory direction is from the genes in the rows to the promoter in corresponding columns Each element of the matrix is their regulation type which is a number chosen from 1 0 1 2 or 2 The elements in the matrix have their certain meanings e 1 only positive regulation e 0 no regulation e 1 only negative regulation e 2 both positiv
7. l of Physical Science School of Engineering Science and School of Information Science and Technology Personally I own great thanks to Jenhan Tao who is a UC Berkeley student and also a clotho developer He helps us solve a lot of problems about coding and connecting to clotho 10
8. r regulatory relations A activates itself and B and B both activates itself and A Then we can figure out A and B s regulatory matrix like this 3 2 How To Input Please follow these steps to enter your data 1 Input your matrix size 2 into the text field and press Confirm 2 A small table with different color will appear within the main table Input the regu latory matrix in the small table The screen shot is Lj Regulon Lib HN pasted on the right File Search Help About side regulator 1 GOES 2 AA 3 alar 4 Qu 5 regulator 6 2 Always using GRN for short 3 3 How To Generate Results Please follow these steps to generate results 1 You can choose Mode 1 or Mode 2 as you like Mode 1 uses Operon Operon database and Mode 2 uses Gene Promoter database 2 If you want to save the results you can click File on the menu bar or click right on the current result tab and choose save Screen shots are pasted below Picture on the left side is the screen shot for using Mode 1 and on the right side using mode 2 The output of Mode 1 includes number of choices and operons names of each choice The output of Mode 2 includes number of choices promoter names of each choice and gene names of each choice File Search Help About Main Page Resulti Result choice 3 Biobrick 1 yebGp mngR Biobrick 2 tsrp1 mirA choice 2587 Biobrick 1 zntAp narP Biobrick 2 fumCp
9. tor 4 3 Entering Regulatee Name There are alse two ways for you to enter your regulator name 1 Enter the regulatee name in the regulatee name text field 2 Choose your regulatee from regulatee table or regulatee candidates table In the demo I continue using the example of the above section You can choose one of the regulatees from the regulatee candidates table of Operon ada alkB For example the Operon aidB is chosen Then aidB will appear in the regulatee name text field and its related regulators will appear in the regulator candidates table in the meantime X Regulatee Lib k ey 3 i N gt Y a iz a a ogt f y o o J ws M hy kd f k y i l d A j i UA ada alkB wT PET f LE ye o o sr e T co ra d e MAD sty wo i o f s N f Regulatees Figure 4 Search Regulatee 4 4 Generating Regulatory Relation If the regulator name and the regulatee name are not null press Search Button the regulatory relation will appear between two text fields In the demo I still use examples stated above After clicking on the Icon a cartoon picture appears indicating positive regulatory relation between ada alkB and aidb For other types of regulatory relations different cartoon pictures will be shown You can have a try Ar yy 4 i OS ASA acna r acrAB TMacrD acrEF acrR Macs yjcH Figure 5 Generate Regulatory Regulation 5 View
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