Team:USTC Software/notebook

From 2010.igem.org

Revision as of 02:45, 13 October 2010

March & April

Zhen Wang

Give our software team a name – bionovo, naming our game – iGAME. Learining from other biology reaction network simulation software – Berkeley Software Team 2009, SynBioSS, TinkerCell, CellDesigner, because the realization of our game need simulation too. Thinking about the big picture of our game, the simulation, the UI, the database, the play modes. (Liao)Chen Liao promoted a way to do the simulation – every biobrick will have an input and an output. Though following discussion proved it was not a great idea, it is a good start for the simulation part of out game.

Kun Jiang

To start our project, I begin a detailed study of biology related softwares, including SynBioSS, CellDesigner and TinkerCell. Especially, TinkerCell is a open source software, so I can read it's source code to carefully research biology simulation software. Those softwares provide me a lot of ideas, direct our development and influence our design.

Luojun Wang

Strict rules for safety have been considered and made.To start our own human practice, previous works have been investigated.

Shangyu Luo

Having made sure that our project will be about a game in synthetic biology, we begin to discuss the components of our software. Basically, we divide it into two parts: fore-end and back-end. I will work on the later one which includes simulation, database, interface, etc. Furthermore, I focus on the model and simulation of biological reactions and try to find a proper method to serve for our project.

MAY

Zhen Wang

May 3 ~ May 9, 2010 Write a PPT on the framework of our game, which focused on database. We came to the conclusion that the database should have the following features, quick search, links to reactions, inheritance between different parts, easy to add elements, and most of them are still suitable now(Aug, 2010).

May 10 ~ May 16, 2010 We decide to realize the database and simulation of a biological oscillator first, the model was presented in article “A synthetic oscillatory network of transcriptional regulators”, Nature 2000.

May 17 ~ Jun 6, 2010 Summarize the reactions of oscillator, learn SBML and libsbml APIs. Search biomodels.net for SBMLs on oscillator created by other people and learn from them.

Kun Jiang

May 3 ~ May 9, 2010 Study the specification document of libsbml make an attempt at developing a sbml ode solver basing on the sundials math library.

May 10 ~ May 16, 2010 After meeting difficulty of developing a sbml ode solver from scratch, We turn to the existing library. At last, soslib v1.6.0, a library covered by the LGPL license, was choose to be as a part of our software. Add simple data display function to the soslib to get curve representation of the output data. And also need be noticed is that the soslib only support sbml version 2 level 1.

May 17 ~ Jun 6, 2010 Figure out the differences between sbml version 2 level 1 specification and sbml version 2 level 4 specification. Because our database input files are based on sbml version 2 level 4.

Luojun Wang

Regular communication and seminars with wet lab team. Different plans for promoting iGAME have been made.

Shangyu Luo

May 3 ~ May 9, 2010 I have had some knowledge of SynBioSS because I made a presentation of a igem team’ work which is the developer of this software. Thus I concentrate on studying another synthetic biology software: TinkerCell

May 10 ~ May 16, 2010 read the source code of TinkerCell and place emphasis on the simulation parts. Try to detail how it operate its modeling in sequence and detect that they use ODE and some mathematic API to simulate the biological reactions.

May 17 ~ Jun 6, 2010 specify the simulation means we will apply. I have collected some information about the methods like deterministic simulation and stochastic simulation. Meanwhile, the reaction network will have three layers: molecular reaction layer, topology layer and mathematical equations layer.

Zhengda He

Study Qt4 , HTML , JavaScript , CSS and some other computer technology , to prepare for the project .

 When we've already decided to make a biological game , I took the charge of designing the story 

of the game , so I moved to it.

JUNE

Zhen Wang

Jun 7 ~ Jun 13, 2010 We find Antimony is a good way to translate SBML files into human readable form, so I read some documents on libsbml. Liao and I discussed on the project of PKU2009, we both agreed the simulation of it will be a tough job.

Jun 14 ~ Jun 20, 2010 I write a PPT on UI and give a draft of my design, the PPT focuses on input and output. The design of input seems pretty good, but we get stuck in output. How should we present the result to players? It is a hard question. We decide to add drag and drop features throughout the game to make it easier to use and play.

Shangyu Luo

Now we have two choices: developing the whole process of simulation and model by ourselves or learn from other existing software and utilize APIs as much as possible Start to learn some knowledge about SBML and libxml as we will use them as format of presentation and interaction.

JULY

Liao Chen

• Liao Chen (7.20): Discuss framework of core programme of simulation part of our project with Jiang

Hao. We decided to take consideration of the structure of complex, which solves problems we encountered when handling reactions with regard to complex molecules.

• Liao Chen (7.21): We decided to model the species (either complex or simple species) using two data

structures:

• 1. ChainList is used to describe chains of DNA, RNA or Protein molecules. Small molecules are also

of such structure with only one element on one chain.

• 1. Tree structure is used to describe binding state of elements of different chains. Children nodes

bind with each other and form their parent node. Thus, other than chains, a species has its binding state forest, which composed of many trees mentioned above.

• Liao Chen (7.22): We decided to store data of species and reactions in XML format.
• Liao Chen (7.23): To search reactions of species includes, we need powerful support of species and

reactions database. But first, we need a database manager to manage our XML data files, which must provide query operation of data we want.

• Liao Chen (7.24): We find it! Oracle Berkeley DB XML! It is a Native XML Database. It is capable of

storing and indexing collections of XML documents in both native and mapped forms for highly efficient querying, transformation, and retrieval.

• Liao Chen (7.25): A well designed database is quite important for our project. Start to design file

organization and format of database files.

• Liao Chen (7.26~7.30): Discussion with Jiang Hao about how to design database. We decide to make 4

file containers to hold different kind of contents:

• 1. global : contains unit definition, definition of standard conditions of cultivating bacterial, and

so on.

• 1. module : module of each species, including biobricks, virtual biobricks, cells, plasmids,

substituents and so on.

• 1. species : each species that occurs in reactions defined in reaction container is defined here.
  2. reactions : reactions of all species defined in species container are defined here.

Zhen Wang

Jul 19 ~ Jul 25, 2010 I Find myself have little knowledge about partregistry, so I read registry and summarize promoter, plasmid backbones, protein coding sequence, degradation reaction, plasmid, etc. The first edition of oscillator database pack and database documentation has been written by Liao, I only give some suggestions on naming our modules, and make little contribution on the whole thing.

Jul 26 ~ Aug 1, 2010 Talk together with Hao Jiang and Liao, write the second edition of oscillator database and database format. In order to deal with the real reactions and real species, we add virtual biobricks to our database, together with a bunch of new attributes. The database is constructed by 3 lists, the single compartment list, the species structure list, the reaction list, relationship of the 3 lists is shown in the following picture.[pic]

Kun Jiang

Study the CMake, a project manage tool for huge software project, and QT, a cross-platform application and UI framework. Try to develop a demo project.

Luojun Wang

Start of our human practice. Summer classes of synthesis biology begin and are lectured by Prof. Haiyan Liu and Jiong Hong, both of who are advisors of our team. After communicating with Prof. Haiyan Liu and Jiong Hong, I decide to do many things along with the curriculum. Surveys are written and done for the synthesis biology class. Lectures are also prepared for it. Much communication with other teams and people is done, which is quite educational and impressive.(it's fun, too!)

Shangyu Luo

Jul 19 ~ Jul 25, 2010 As the problem with simulation has finally been solved, I turn to acquire some knowledge about database which will be a huge and basic part of our project and then begin a long period cooperation with Zhen Wang. Obtain the classification of database: network database, hierarchical database, relational database

Jul 26 ~ Aug 1, 2010 have a general idea of database and have a discussion with Hao Jiang, Zhen Wang, Chen Liao frequently to deal with some difficulties in the construction of database, as well as some biological problem.

AUGUST

Chen Liao

• Liao Chen (8.1): Start writing core codes of our project.

• Liao Chen (8.2~8.12): Construct MySpecies class whose objects are equivalent to real species in

biological system. Five modifications have been made until the final version.

software 

dbxml

• Liao Chen (8.25, afternoon): leave for shanghai to get our passport visaed. We played Three Kingdom

Kills (TKK) on the train. The speed of the train is as slow as a turtle creeps.

• Liao Chen (8.25, night): So many pretty, tall girls outside of Rolex faced to HuangPu river... what

a feel if...

• Liao Chen (8.26): Face to face with visa officer. Three checked, 10 passed.

Zhen Wang

Aug 2 ~ Aug 15, 2010 At first we want to use MySQL to manage our database, later we find Berkeley DBXML is a better tool, so I studied on how to use DBXML. Kun Jiang quickly write an interface using DBXML API and a small PDF instruction, code genius! Finish database format v3.0 – the 3rd version of database, now there are 4 lists, the global, the module, the species, the reactions. Global list stores data that must be pre-defined. Specify database format and give detailed examples on each list. In order to realize the real species, we add substituent in module and chain in species(special thanks to Hao Jiang).

Aug 16 ~ Aug 22, 2010 Read more documents on DBXML and XML. Prepare materials for interview in Shanghai. Liao upload the first version of iGAME core, Soimort upload the first version of iGAME web UI, this is a big motivation to me, seems our game will be able to work finally.

Aug 23 ~ Aug 29, 2010 Prepare materials for interview in Shanghai. All iGEM USTC TEAM members go to Shanghai for visa interview, I pass, but 3 of our member are checked, best wishes for them! Refine the database format, specify bioreactor in module list, compartment&condition in reaction list, substituent changes in species list(special thanks to Hao Jiang). We receive our passports with visas one by one. Draw a couple of charts and diagrams to explain the construction of database, seems I am pretty good at it.[pic] Finish and upload database format PDF and database RAR v8.27, together with some photos taken at Shanghai. Realize work log is very important, so recall my work and write my notebook.

Kun Jiang

Aug 2 ~ Aug 22, 2010 Study the dbxml specification document for developing a more convenience database interface.

Aug 23 ~ Aug 29, 2010 Make preparation for visa interview in Shanghai.

Luojun Wang

Collaboration with Prof. Jiong Hong features the synthesis biology class with IGEM issues and our program. Lectures on ethnics and promotions for iGAME are given during the curriculum, which are partly videotaped. : ) Surveys are also made for iGAME. Statistics have been analysized in many different ways before CIRCOS software runs into my sight. Methods of plotting chromesomes are used in the demonstration of the work, which is the most innovative idea I have ever seen in any performance of survey.:D In the poll on favorite game type, adventure game is on top, can we make a tutor game like Prince of Persia?lol~ Interviewed by Yueyue Zhang, doctor of BIOS Centre of London School of Economics and Politics Science. Opinions on human practice have been exchanged and much new information is obtained from her.(Special thanks to her!)

Shangyu Luo

Aug 2 ~ Aug 15, 2010 With Zhen Wang coming up with different generations of database, I make some discussion with him and help him to modify, specify and complement our database

Aug 16 ~ Aug 22, 2010 Start to learn how to utilize dbxml to aid us in the construction of our database. Be familiar with the environment and command of this software and scan the code to capture the basic features of it which will contribute to handling its APIs in our software Try to learn how to add contents of our team’s wiki

Aug 23 ~ Aug 29, 2010 Use 2009 Minnesota igem team as a trial, I list out all the materials we need in our database but detect that there are some details we can not cover in our database. Try to tackle with this problem with Chen Liao. What’s more, I apply for some financial aid or fund for my trip to MIT and fortunately I get it from my own department: School of Computer Science and Technology! Thanks to the support of my department, I can get a chance to America, to MIT, so I have to express my appreciation again! Though it is just founded before long and doesn’t have much finance at present, my school gives great supports to students and aids them to expand the horizon and improve their abilities in comprehensive fields. With a lot of young but full of research background teachers and professors, I think my school will have a bright future!

SEPTEMBER

Zhen Wang

Aug 30 ~ Sep 5, 2010 Plan: Think about what database modification tool a senior user would like to use. Write full database that includes the whole oscillator. Read more on XML. Have fun working.

Summary: Not having much fun working, with both sides’ tasks to be done. Full database for oscillator is done 2010/9/2. I haven’t checked it in detail yet. It is very likely we are going to change the db structure yet again, good thing though. Learn from libsbml the sbml modification tool, our db modification should somehow like that. It should focus on adding and constructing new model. Discuss on UI&input with Liao, writing the new UI draft.

Sep 5 ~ Sep 12, 2010 Plan: Discuss UI&input with Soimort. Discuss ODE solver with Kun. Teaching junior students how to write DB. Have fun working.

Summary: This is a crazy week for me! Together with Liao, we make huge modifications on the structure of for at least 3 times! We change the xml structure for storing data, revise the attributes on each item, and have heated debate on our standard of bio-modeling. At first the modification process seems endless, but by the end of the week, we have come to agreement on most of the details. This gives me a lot of hope, and this week has definitely been a big leap for our DB. This time Liao finally realizes that we are actually making the next-generation standard of SBML, haha. Settling a brand-new standard of bio-modeling has actually become the core of our work. As far as I’m concerned, we have made 3 shifts on our goal, UI -> simulation -> bio-modeling standard, this is poor goal-setting, we didn’t make a clear map of what we are doing at the very beginning. I talk on DB and modeling with 2 junior students, they are all confident and eager to learn, I think they can handle it properly very soon. I just don’t have the time to talk with Soimort and Kun.

Sep 12 ~ Sep 19, 2010 Plan: Write note on UI&input, discuss UI&input with Soimort. Discuss ODE solver with Kun. Settle the final edition of DB. Writing DB of EPF-Lausanne with 2 junior students. Have fun working.

Summary: Write a detailed note on UI&Input and discuss it with Soimort. I believe it is not easy for him to understand the whole design of UI&Input and its connection with the database, I should spend more time to explain the details for him. Kun says he has finished the L2V4 update of ODE solver, he is now working on the boolean value judging module which will be used in Liao’s code. Liao’s first edition of document on DB standard is done, it’s now my turn to refine it and fix the bugs. Zhengda He has written part of the DB of EPF-Lausanne 2009 under my guidance, we can see the whole DB by next week, hopefully. Another junior student Zhaoyi Li is working on synchronized E.coli oscillator, a biological breakthrough published on Nature 2009. Last but not least, this is a busy week for scheduling trip, paying fee and talking to sponsor. Handling these things cost me lots of time, we should have a secretary for this, luckily we find one, she is Jue Wang. My boss doesn’t push me so hard on finishing his assignment, and I’m grateful for that, he must know that I don’t have much time. I do have fun working this week!

Sep 20 ~ Sep 26, 2010 Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Discuss UI with Soimort and push him to work faster, discuss synchronized E.coli with Zhaoyi Li. Have fun working.

Summary: Today is Oct 7, and I have just start writing work summary of the last week in Sep. During last 2 weeks we celebrated Mid-Autumn Festival and had 7 day off for National Day, while others are enjoying themselves traveling, we iGEM team members didn’t take a day off. We have to seize every minute to make our software work! I guess I’m just too busy to write my work log, and right now I am trying my best to recall what exactly I did in the last week of Sep…

Here’s what I can remember.

Zhaoyi Li looked into the nature article on synchronized ecoli clock and gave a brief lecture, then he started to analyze all the reaction and species in the model, and prepare to write the DB of it. Zhengda He’s parents came to see him, so he disappeared for 3 days or so. He has finished part of EPF-Lausanne DB but not all, so Yubo Qi kicked in to investigate the proper parameters for reaction. Unfortunately, it’s almost a hopeless task, no reliable source with specified parameters can be found, so we gave up at last.

I finished another detail draft on input UI design, and Soimort is constructing our UI according to it. I tried to discuss more with Soimort and push him harder, but can’t find the right way…

My girlfriend came and we spent 3 days together. It was 3 halves of days actually, since there are tasks I cannot put aside. However, she was so thoughtful and supportive, and didn’t complain about my absence. We had our sweet moments together. Her visiting means a lot to me, and fuels me up with energy to work on.

Kun Jiang

Sep 5 ~ Sep 12, 2010 Build two tool softwares to help Zhen Wang to edit our database input files.

Sep 12 ~ Sep 30, 2010 Modify the soslib v1.6.0 source code to base on libsbml v4.0.1, Which enable soslib support sbml version2 level 4 to meet our database format requirements.

Summary: (we will see~)

Luojun Wang

Idea of starting a community has been discussed with the wet team and will be realized soon. Concerned with IPR issue, I consult the IPRs Centre of USTC for safety of iGAME. Start of wiki scripts.

Summary: Finally, I decide to give a name to the human practice project, "the C project". "C" stands for "curriculum","communication" and "community", it is also cool, huh?

Shangyu Luo

I am in Hong Kong now! Thanks to school of computer again! I obtain a chance to live and study in Hong Kong for one semester! Though there is much to do and I have to get familiar with the environment in Hong Kong, I try my best to find time for our project. I skim most of igem teams in latest three years and list some teams whose work can show the advantages and innovations of our database. Their works are about some biological reactions related to light, temperature, PH, etc. Read a paper of Nature about synchronized Ecoli clock, try to master the idea of it and list the reactions in it. It will be added into our database.

OCTOBER

ZHEN WANG

Sep 27 ~ Oct 7, 2010 Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Settle the DB format for good(hopefully).

Summary: As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development.

Most of our team members work intensively during the 7 days off, and the achievement of their work is rich. DB of both EFP-Lausanne and Synchronized Ecoli are basically finished. Tables and graphs on DB structure has been published. Our software core seems finally begin to function right. UI is under constructing. All the codes are now on github.

We schedule our trip and book plane tickets to Beijing, Chicago and Boston. Jue Wang is now in charge of money and team wear.

We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.

Lab Notebook

Meetings are set every Saturday since Feb.15th, then three more discussions (Mon, Wes, Fri) are added when we start to determine our project since Mar 21th.

• 2010.4.10 – 2010.5.14 reports of the former iGEM works

• 2010.5.21 – 2010.6.11 broach of candidate projects
  • cell density control
  • Reporter and imaging
  • DNA writing and reading in the cell
  • Biodegradation of plastics

• 2010.6.12 – 2010.6.30 further research by small groups on

the candidate projects

• sketch map of our final project host-cell free reaction

chamber was set up

All the reports information, slides and audio records of our meetings are arranged here.