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- | __NOTOC__
| + | {{Team:USTC_Software/Header}} |
- | ==''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.
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- | 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
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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===
| + | |
- | 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.
| + | |
- | | + | |
- | === Luojun Wang ===
| + | |
- | 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''==
| + | |
- | ===Zhen Wang===
| + | |
- | 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.
| + | |
- | | + | |
- | May 17 ~ Jun 6, 2010
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- | 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.
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- | 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.
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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.
| + | |
- | | + | |
- | === Luojun Wang ===
| + | |
- | Regular communication and seminars with wet lab team. Different plans for promoting iGAME have been
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- | made.
| + | |
- | | + | |
- | ==''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
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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
| + | |
- | of input seems pretty good, but we get stuck in output. How should we present the result to players?
| + | |
- | 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.
| + | |
- | | + | |
- | ==''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:
| + | |
- | *# 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.
| + | |
- | *# 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.
| + | |
- | *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:
| + | |
- | *#global : contains unit definition, definition of standard conditions of cultivating bacterial, and
| + | |
- | 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.
| + | |
- | | + | |
- | ===Zhen Wang===
| + | |
- | Jul 19 ~ Jul 25, 2010
| + | |
- | 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.
| + | |
- | 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
| + | |
- | 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
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- | 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
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- | application and UI framework. Try to develop a demo project.
| + | |
- | | + | |
- | === Luojun Wang ===
| + | |
- | 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
| + | |
- | 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!)
| + | |
- | | + | |
- | ==''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
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- | 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!)
| + | |
- | | + | |
- | ==''SEPTEMBER''==
| + | |
- | ===Zhen Wang===
| + | |
- | Aug 30 ~ Sep 5, 2010
| + | |
- | Plan:
| + | |
- | 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.
| + | |
- | Have fun working.
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- | | + | |
- | 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.
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- | 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.
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- | | + | |
- | 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,
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- | 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
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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
| + | |
- | 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
| + | |
- | Plan:
| + | |
- | 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.
| + | |
- | | + | |
- | ===Kun Jiang===
| + | |
- | Sep 5 ~ Sep 12, 2010
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- | Build two tool softwares to help Zhen Wang to edit our database input files.
| + | |
- | | + | |
- | 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:
| + | |
- | (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.
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- | Start of wiki scripts.
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- | | + | |
- | Summary:
| + | |
- | 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 ==
| + | |
| <html> | | <html> |
| <style type="text/css"> | | <style type="text/css"> |
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| </style> | | </style> |
| </html> | | </html> |
| + | ==Monthly Notebook== |
| + | {| style="background-color:white; " align="center" border="1" |
| + | |-valign="top" |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_3 March] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_4 April] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_5 May] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_6 June] |
| + | |-valign="top" |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_7 July] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_8 August] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_9 September] |
| + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_10 October] |
| + | |} |
| | | |
- | Meetings are set every Saturday since Feb.15th, then three
| + | ==Daily Notebook== |
- | more discussions (Mon, Wes, Fri) are added when we start to
| + | {| style="background-color:#ffffff;" align="center" border="1"" |
- | 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
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- | ** Reporter and imaging
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- | ** DNA writing and reading in the cell
| + | |
- | ** Biodegradation of plastics
| + | |
- | | + | |
- | *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
| + | |
- | chamber was set up
| + | |
- | | + | |
- | All the reports information, slides and audio records of our
| + | |
- | meetings are arranged here.
| + | |
- | | + | |
- | {| style="background-color:#ffffcc;" | + | |
- | |align="center" border="1""
| + | |
| |-valign="top" | | |-valign="top" |
- | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
| |
- | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2009 |month=12 }}
| |
- | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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- | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=01 }}
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- | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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- | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=02 }}
| |
| |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=03 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=03 }} |
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| |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=05 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=05 }} |
- | |-valign="top"
| |
| |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=06 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=06 }} |
| + | |-valign="top" |
| |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=07 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=07 }} |