Team:USTC Software/notebook

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__NOTOC__
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{{Team:USTC_Software/Header}}
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==''March & April''==
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===Zhen Wang===
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Give our software team a name – bionovo, naming our game – iGAME.
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Learining from other biology reaction network simulation software – Berkeley Software Team 2009,
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SynBioSS, TinkerCell, CellDesigner, because the realization of our game need simulation too.
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Thinking about the big picture of our game, the simulation, the UI, the database, the play modes.
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(Liao)Chen Liao promoted a way to do the simulation – every biobrick will have an input and an
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output. Though following discussion proved it was not a great idea, it is a good start for the
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simulation part of out game.
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===Kun Jiang===
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To start our project, I begin a detailed study of biology related softwares, including SynBioSS,
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CellDesigner and TinkerCell. Especially, TinkerCell is a open source software, so I can read it's
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source code to carefully research biology simulation software.  Those softwares provide me a lot of
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ideas, direct our development and influence our design.
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=== Luojun Wang ===
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Strict rules for safety have been considered and made.To start our own human practice, previous
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works have been investigated.
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==''MAY''==
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===Zhen Wang===
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May 3 ~ May 9, 2010
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Write a PPT on the framework of our game, which focused on database. We came to the conclusion that
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the database should have the following features, quick search, links to reactions, inheritance
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between different parts, easy to add elements, and most of them are still suitable now(Aug, 2010).
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May 10 ~ May 16, 2010
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We decide to realize the database and simulation of a biological oscillator first, the model was
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presented in article “A synthetic oscillatory network of transcriptional regulators”, Nature 2000.
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May 17 ~ Jun 6, 2010
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Summarize the reactions of oscillator, learn SBML and libsbml APIs. Search biomodels.net for SBMLs
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on oscillator created by other people and learn from them.
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===Kun Jiang===
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May 3 ~ May 9, 2010
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Study the specification document of libsbml make an attempt at developing a sbml ode solver basing
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on the sundials math library.
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May 10 ~ May 16, 2010
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After meeting difficulty of developing a sbml ode solver from scratch, We turn to the existing
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library. At last, soslib v1.6.0, a library covered by the LGPL license, was choose to be as a part
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of our software.
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Add simple data display function to the soslib to get curve representation of the output data. And
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also need be noticed is that the soslib only support sbml version 2 level 1.
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May 17 ~ Jun 6, 2010
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Figure out the differences between sbml version 2 level 1 specification and sbml version 2 level 4
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specification. Because our database input files are based on sbml version 2 level 4.
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=== Luojun Wang ===
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Regular communication and seminars with wet lab team. Different plans for promoting iGAME have been
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made.
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==''JUNE''==
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===Zhen Wang===
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Jun 7 ~ Jun 13, 2010
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We find Antimony is a good way to translate SBML files into human readable form, so I read some
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documents on libsbml. Liao and I discussed on the project of PKU2009, we both agreed the simulation
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of it will be a tough job.
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Jun 14 ~ Jun 20, 2010
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I write a PPT on UI and give a draft of my design, the PPT focuses on input and output. The design
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of input seems pretty good, but we get stuck in output. How should we present the result to players?
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It is a hard question.
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We decide to add drag and drop features throughout the game to make it easier to use and play.
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==''JULY''==
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===Liao Chen===
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*Liao Chen (7.20): Discuss framework of core programme of simulation part of our project with Jiang
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Hao. We decided to take consideration of the structure of complex, which solves problems we
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encountered when handling reactions with regard to complex molecules.
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*Liao Chen (7.21): We decided to model the species (either complex or simple species) using two data
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structures:
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*# ChainList is used to describe chains of DNA, RNA or Protein molecules. Small molecules are also
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of such structure with only one element on one chain.
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*# Tree structure is used to describe binding state of elements of different chains. Children nodes
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bind with each other and form their parent node. Thus, other than chains, a species has its binding
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state forest, which composed of many trees mentioned above.
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*Liao Chen (7.22): We decided to store data of species and reactions in XML format.
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*Liao Chen (7.23): To search reactions of species includes, we need powerful support of species and
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reactions database. But first, we need a database manager to manage our XML data files, which must
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provide query operation of data we want.
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*Liao Chen (7.24): We find it! Oracle Berkeley DB XML! It is a Native XML Database. It is capable of
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storing and indexing collections of XML documents in both native and mapped forms for highly
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efficient querying, transformation, and retrieval.
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*Liao Chen (7.25): A well designed database is quite important for our project. Start to design file
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organization and format of database files.
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*Liao Chen (7.26~7.30): Discussion with Jiang Hao about how to design database. We decide to make 4
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file containers to hold different kind of contents:
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*#global : contains unit definition, definition of standard conditions of cultivating bacterial, and
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so on.
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*#module : module of each species, including biobricks, virtual biobricks, cells, plasmids,
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substituents and so on.
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*#species : each species that occurs in reactions defined in reaction container is defined here.
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*#reactions : reactions of all species defined in species container are defined here.
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===Zhen Wang===
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Jul 19 ~ Jul 25, 2010
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I Find myself have little knowledge about partregistry, so I read registry and summarize promoter,
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plasmid backbones, protein coding sequence, degradation reaction, plasmid, etc.
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The first edition of oscillator database pack and database documentation has been written by Liao, I
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only give some suggestions on naming our modules, and make little contribution on the whole thing.
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Jul 26 ~ Aug 1, 2010
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Talk together with Hao Jiang and Liao, write the second edition of oscillator database and database
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format. In order to deal with the real reactions and real species, we add virtual biobricks to our
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database, together with a bunch of new attributes. The database is constructed by 3 lists, the
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single compartment list, the species structure list, the reaction list, relationship of the 3 lists
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is shown in the following picture.[pic]
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===Kun Jiang===
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Study the CMake, a project manage tool for huge software project, and QT, a cross-platform
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application and UI framework. Try to develop a demo project.
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=== Luojun Wang ===
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Start of our human practice.
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Summer classes of synthesis biology begin and are lectured by Prof. Haiyan Liu and Jiong Hong, both
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of who are advisors of our team.
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After communicating with Prof. Haiyan Liu and Jiong Hong, I decide to do many things along with the
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curriculum.
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Surveys are written and done for the synthesis biology class. Lectures are also prepared for it.
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Much communication with other teams and people is done, which is quite educational and
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impressive.(it's fun, too!)
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==''AUGUST''==
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===Chen Liao===
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*Liao Chen (8.1): Start writing core codes of our project.
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----
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*Liao Chen (8.2~8.12): Construct MySpecies class whose objects are equivalent to real species in
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biological system. Five modifications have been made until the final version.
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----
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;software : dbxml
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*Liao Chen (8.25, afternoon): leave for shanghai to get our passport visaed. We played Three Kingdom
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Kills (TKK) on the train. The speed of the train is as slow as a turtle creeps.
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*Liao Chen (8.25, night): So many pretty, tall girls outside of Rolex faced to HuangPu river... what
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a feel if...
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*Liao Chen (8.26): Face to face with visa officer. Three checked, 10 passed.
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===Zhen Wang===
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Aug 2 ~ Aug 15, 2010
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At first we want to use MySQL to manage our database, later we find Berkeley DBXML is a better tool,
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so I studied on how to use DBXML. Kun Jiang quickly write an interface using DBXML API and a small
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PDF instruction, code genius!
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Finish database format v3.0 – the 3rd version of database, now there are 4 lists, the global, the
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module, the species, the reactions. Global list stores data that must be pre-defined. Specify
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database format and give detailed examples on each list.
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In order to realize the real species, we add substituent in module and chain in species(special
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thanks to Hao Jiang).
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Aug 16 ~ Aug 22, 2010
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Read more documents on DBXML and XML.
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Prepare materials for interview in Shanghai.
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Liao upload the first version of iGAME core, Soimort upload the first version of iGAME web UI, this
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is a big motivation to me, seems our game will be able to work finally.
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Aug 23 ~ Aug 29, 2010
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Prepare materials for interview in Shanghai.
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All iGEM USTC TEAM members go to Shanghai for visa interview, I pass, but 3 of our member are
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checked, best wishes for them!
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Refine the database format, specify bioreactor in module list, compartment&condition in reaction
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list, substituent changes in species list(special thanks to Hao Jiang).
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We receive our passports with visas one by one.
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Draw a couple of charts and diagrams to explain the construction of database, seems I am pretty good
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at it.[pic]
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Finish and upload database format PDF and database RAR v8.27, together with some photos taken at
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Shanghai.
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Realize work log is very important, so recall my work and write my notebook.
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===Kun Jiang===
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Aug 2 ~ Aug 22, 2010
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Study the dbxml specification document for developing a more convenience database interface.
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Aug 23 ~ Aug 29, 2010
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Make preparation for visa interview in Shanghai.
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===Luojun Wang===
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Collaboration with Prof. Jiong Hong features the synthesis biology class with IGEM issues and our
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program.
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Lectures on ethnics and promotions for iGAME are given during the curriculum, which are partly
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videotaped. : )
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Surveys are also made for iGAME.
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Statistics have been analysized in many different ways before CIRCOS software runs into my sight.
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Methods of plotting chromesomes are used in the demonstration of the work, which is the most
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innovative idea I have ever seen in any performance of survey.:D In the poll on favorite game type,
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adventure game is on top, can we make a tutor game like  ''Prince of Persia''?lol~
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Interviewed by Yueyue Zhang, doctor of BIOS Centre of London School of Economics and Politics
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Science. Opinions on human practice have been exchanged and much new information is obtained from
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her.(Special thanks to her!)
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==''SEPTEMBER''==
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===Zhen Wang===
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Aug 30 ~ Sep 5, 2010
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Plan:
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Think about what database modification tool a senior user would like to use.
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Write full database that includes the whole oscillator.
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Read more on XML.
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Have fun working.
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Summary:
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Not having much fun working, with both sides’ tasks to be done.
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Full database for oscillator is done 2010/9/2. I haven’t checked it in detail yet.
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It is very likely we are going to change the db structure yet again, good thing though.
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Learn from libsbml the sbml modification tool, our db modification should somehow like that. It
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should focus on adding and constructing new model.
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Discuss on UI&input with Liao, writing the new UI draft.
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Sep 5 ~ Sep 12, 2010
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Plan:
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Discuss UI&input with Soimort.
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Discuss ODE solver with Kun.
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Teaching junior students how to write DB.
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Have fun working.
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Summary:
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This is a crazy week for me! Together with Liao, we make huge modifications on the structure of for
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at least 3 times! We change the xml structure for storing data, revise the attributes on each item,
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and have heated debate on our standard of bio-modeling. At first the modification process seems
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endless, but by the end of the week, we have come to agreement on most of the details. This gives me
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a lot of hope, and this week has definitely been a big leap for our DB.
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This time Liao finally realizes that we are actually making the next-generation standard of SBML,
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haha. Settling a brand-new standard of bio-modeling has actually become the core of our work. As far
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as I’m concerned, we have made 3 shifts on our goal, UI -> simulation -> bio-modeling standard, this
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is poor goal-setting, we didn’t make a clear map of what we are doing at the very beginning.
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I talk on DB and modeling with 2 junior students, they are all confident and eager to learn, I think
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they can handle it properly very soon.
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I just don’t have the time to talk with Soimort and Kun.
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Sep 12 ~ Sep 19, 2010
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Plan:
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Write note on UI&input, discuss UI&input with Soimort.
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Discuss ODE solver with Kun.
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Settle the final edition of DB.
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Writing DB of EPF-Lausanne with 2 junior students.
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Have fun working.
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Summary:
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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.
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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.
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Liao’s first edition of document on DB standard is done, it’s now my turn to refine it and fix the bugs.
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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.
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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.
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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.
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I do have fun working this week!
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===Kun Jiang===
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Sep 5 ~ Sep 12, 2010
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Build two tool softwares to help Zhen Wang to edit our database input files.
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Sep 12 ~ Sep 30, 2010
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Modify the soslib v1.6.0 source code to base on libsbml v4.0.1, Which enable soslib support sbml
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version2 level 4 to meet our database format requirements.
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Summary:
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(we will see~)
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===Luojun Wang===
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Idea of starting a community has been discussed with the wet team and will be realized soon.
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Concerned with IPR issue, I consult the IPRs Centre of USTC for safety of iGAME.
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Start of wiki scripts.
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Summary:
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Finally, I decide to give a name to the human practice project, "the C project". "C" stands for
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"curriculum","communication" and "community", it is also ''cool'', huh?
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== Lab Notebook ==
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==Monthly Notebook==
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{| style="background-color:white; " align="center" border="1"
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|-valign="top"
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_3 March]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_4 April]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_5 May]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_6 June]
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|-valign="top"
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_7 July]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_8 August]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_9 September]
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_10 October]
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|}
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Meetings are set every Saturday since Feb.15th, then three
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==Daily Notebook==
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more discussions (Mon, Wes, Fri) are added when we start to
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determine our project since Mar 21th.
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*2010.4.10 – 2010.5.14  reports of the former iGEM works
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*2010.5.21 – 2010.6.11  broach of candidate projects
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** cell density control
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** Reporter and imaging
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** DNA writing and reading in the cell
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** Biodegradation of plastics         
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*2010.6.12 – 2010.6.30  further research by small groups on
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the candidate projects
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* sketch map of our final project host-cell free reaction
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chamber was set up
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All the reports information, slides and audio records of our
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meetings are arranged here.
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{| style="background-color:#ffffff;" align="center" border="1""
{| style="background-color:#ffffff;" align="center" border="1""
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|{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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|-valign="top"
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|{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
|title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=08 }}
|title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=08 }}

Latest revision as of 20:58, 25 October 2010

Monthly Notebook

March April May June
July August September October

Daily Notebook

March
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Retrieved from "http://2010.igem.org/Team:USTC_Software/notebook"