Team:USTC Software/notebook

From 2010.igem.org

Revision as of 08:31, 1 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 tocarefully research biology simulation software. Those softwares provide me a lot of ideas, direct our development and influence our design.

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, 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.

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.

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.
  2. 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.
  2. module : module of each species, including biobricks, virtual biobricks, cells, plasmids, substituents and so on.
  3. species : each species that occurs in reactions defined in reaction container is defined here.
  4. 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.

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.

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.

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~)