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Team:Groningen/Project Plan/Tools and Documentation
From 2009.igem.org
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| - | [[Category:Team:Groningen/Disciplines/Configuration_and_Change_Management| | + | {{Team:Groningen/Project_Plan/Header}} |
| - | [[Category:Team:Groningen/Roles/Configuration_Manager| | + | [[Category:Team:Groningen/Disciplines/Configuration_and_Change_Management|Tools and Documentation]] |
| - | [[Category:Team:Groningen/Roles/Facility_Manager| | + | [[Category:Team:Groningen/Roles/Configuration_Manager|Tools and Documentation]] |
| - | + | [[Category:Team:Groningen/Roles/Facility_Manager|Tools and Documentation]] | |
| - | + | ||
| - | + | [[Team:Groningen|Our project]] produces [[Team:Groningen/Project_Plan#Deliverables|many artifacts]], this [http://www.upedu.org/upedu/process/artifact/ar_cmpln.htm Configuration Management Plan] (called Tools and Documentation to avoid a lot of jargon) details what tools and processes we use to create these artifacts. Both for dry work and wet work. Do we use Matlab or Mathematica? What programming conventions do we use? Which lab space do we use? When do we use it? | |
| - | [ | + | |
| - | + | Basically anyone may change anything at any time for any reason, and the Configuration Manager keeps an eye on how (and how much) the Wiki and the SVN repository are used. He also writes this document (assisted by the Facility Manager(s) and others for lab-specific parts). | |
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| - | = | + | <html><style type="text/css"> |
| - | + | .wetwork { color: green; } | |
| - | + | </style></html> | |
| - | + | ==Tools, Environment, and Infrastructure== | |
| - | + | ===Modelling=== | |
| - | + | <blockquote> | |
| - | + | Describe the computing environment and software tools to be used in fulfilling the CM functions throughout the project or product lifecycle. | |
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Describe the tools and procedures required used to version control configuration items generated throughout the project or product lifecycle. | Describe the tools and procedures required used to version control configuration items generated throughout the project or product lifecycle. | ||
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*anticipated size of product data | *anticipated size of product data | ||
*distribution of the product team | *distribution of the product team | ||
| - | *physical location of servers and client machines | + | *physical location of servers and client machines |
| + | </blockquote> | ||
| - | + | Most documents are created on the Wiki, which has built-in version control features (a revision history, including comments). For Google Docs the same is true. Our network drive does NOT have version control and should not be used for documents that have to be modified (much). For storing/exchanging Matlab code we will use [http://subversion.tigris.org/ Subversion] in combination with [http://code.google.com/ Google Code]. All team members wishing to alter models/write matlab code should follow the following steps to get set up (focusses on Windows): | |
| - | + | # Download and install Matlab R2009a. (Login and click on My Account, both in the upper-right corner, then click on "My Products / Get Licensed Products and Updates".) | |
| + | # Download and install TortoiseSVN: http://tortoisesvn.net/downloads | ||
| + | # Checkout the URL https://igemgroningen.googlecode.com/svn/trunk/ using TortoiseSVN by right-clicking in your iGEM directory (in Windows Explorer) and choosing SVN Checkout. Note that you will have to supply the password that can be found on http://code.google.com/hosting/settings. | ||
| - | + | Whenever you want to make changes to some of the files in the repository, first update all files by choosing SVN Update from the right-click menu in Windows Explorer (this will download any new changes from others), then make your changes, and finish by committing (again through the right-click menu). Do not forget to supply a commit message explaining the changes. | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | Also, in case of conflicts in a Simbiology project you are in trouble (this happens when two people update/change/commit a file at the same time). Unfortunately Mathworks chose to save their projects as one big compressed file, which makes it extremely hard to compare two versions of a project, let alone resolve conflicts. Using [http://winmerge.org/ WinMerge] (with the 7-Zip plugin) these project files can be compared, but you still can't resolve conflicts. So, please stick to one model per project and try to avoid conflicts. If a conflict does occur, contact Jasper for help in resolving it. | |
| - | + | A list of programs that support SBML and there respective capabilities are here [http://sbml.org/SBML_Software_Guide]./SBML_Software_Matrix | |
| - | + | Finally, team members that do '''NOT''' write code can checkout the models using TortoiseSVN in the same way as described above and file issues in the [http://code.google.com/p/igemgroningen/issues/list issue list]. | |
| - | [ | + | |
| - | + | ===Wet Work=== | |
| - | + | *Tools: | |
| - | + | **Ligation ratio: Cloning Tool 6.0 (ask Frans/Sven) | |
| + | **List of used lab tools (and from whom we got them) can be found on GoogleDocs (in Dutch): Lab benodigdheden | ||
| + | *Environment: | ||
| + | **Lab room D113 in Haren | ||
| + | *Infrastructure: | ||
| + | **Archives: Binders for primer sheets, Articles on the subprojects | ||
| + | **Databases used are [http://openwetware.org/wiki/Main_Page OpenWetWare], [http://www.partsregistry.org/Main_Page Part], [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Groningen Sandbox],[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed] | ||
| + | |||
| + | ===Human Practice=== | ||
| + | A survey was made and executed. The consideration and results can be found [https://2009.igem.org/Team:Groningen/Ethics/Survey here] | ||
| + | |||
| + | ==Documentation== | ||
| + | ====Identification Methods==== | ||
| + | Private files are stored in a central repository (currently the Y-drive or Google Docs). Agendas and minutes are stored in their respective folders under the date of the meeting in yyyy-mm-dd format to enable easy sorting. Other documents should be named according to the UPEDU standard as much as possible and prefixed by a short abbreviation in brackets (which makes it easy to reference them), for example [PP] for this document. | ||
| + | |||
| + | All documents that are not necessarily private should be placed on the Wiki under the name of the [http://www.upedu.org/upedu/process/artifact/ovu_arts.htm relevant artifact] (also see the [http://www.upedu.org/upedu/process/artifact/tmpl_cs/ovu_tmplcs.htm list of templates]), always prefixed by Team:Groningen (for example [[Team:Groningen/Vision]]). Images can also be uploaded to the Wiki to accompany texts, but the Wiki should not be used as a general means of exchanging files (for this the Y-drive, Google Docs or Google Groups are more suitable). | ||
| + | |||
| + | Finally note that any changes to documents on the Wiki should make use of the Summary field below the large edit text box to describe the change (it would be nice if you tick the "This is a minor edit" checkbox if you're making small tweaks, like correcting a spelling mistake). These descriptions can be long, or as short as one word, depending on the situation. Afterwards it should be possible to reasonably easily get an overview of how the document evolved, and to look up specific changes. For documents not on the Wiki a Revision History should be present at the top of the document. | ||
| + | |||
| + | ===={{anchor|DirectoryStructure}} Master of Lists==== | ||
| + | {{done}}: Anything about lab stuff (in green!) | ||
*Our wiki | *Our wiki | ||
| Line 72: | Line 75: | ||
***Optionally a photograph | ***Optionally a photograph | ||
***Categories for each of the roles he/she has. | ***Categories for each of the roles he/she has. | ||
| + | **Any JavaScript on the Wiki should (as much as possible/desirable) be written in a separate page and included using a script tag with a href attribute referencing the raw version of the page (see [[:Template:Team:Groningen/Header]] for an example), this avoids problems with ampersands, keeps the pages a bit cleaner and makes it possible for browsers to cache long scripts. When it makes sense the page should be a subpage of the page it is used in. | ||
| + | **[https://2009.igem.org/Team:Groningen/Parts Parts list]: <span class="wetwork">List of glycerol stocks in -80 freezer C from MolGen, also the Quality control by PCR and Restriction analysis should be filled in here.</span> | ||
| + | |||
| + | *Subversion repository | ||
| + | **The trunk is at https://igemgroningen.googlecode.com/svn/trunk/ | ||
| + | **[https://igemgroningen.googlecode.com/svn/trunk/glucose/ /trunk/glucose/] | ||
| + | ***The models for the glucose sensing idea (which we're not pursuing any further). | ||
| + | **[https://igemgroningen.googlecode.com/svn/trunk/buoyant/ /trunk/buoyant/] | ||
| + | ***[[Team:Groningen/Modelling|Models]] (mostly .sbproj files) for the [[Team:Groningen/Vision|buoyant bacteria]]. | ||
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*Google Docs | *Google Docs | ||
**Unfortunately Google Docs does not allow sharing of a directory structure. | **Unfortunately Google Docs does not allow sharing of a directory structure. | ||
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**Minutes and agendas. | **Minutes and agendas. | ||
**Availability of team members. | **Availability of team members. | ||
| - | ** | + | **Balance sheet: estimated costs for tickets, hotel, lab etc and estimated sponsoring. |
| + | **<span class="wetwork">Primers: list with ordering date and concentration of the primers when they did arrive (also for oligo's). | ||
| + | **<span class="wetwork">Chemicals / Materials taken from MolGen: list with all chemicals, materials, enzymes taken from MolGen | ||
| + | **<span class="wetwork">Fridge/Freezer Stock list: list with different sheets for general stocks in the fridge and freeze, additionally a sheet for -20 freezer stocks of all labworkers. | ||
| + | **<span class="wetwork">Lab tools: list of all the stuff (machines, pipettes, etc) we use from microbiology and practicum pool (Labbenodigdheden). | ||
*Y-drive | *Y-drive | ||
**The transfer documents. | **The transfer documents. | ||
**Literature? | **Literature? | ||
**Miscellaneous files | **Miscellaneous files | ||
| - | + | {{Team:Groningen/Project_Plan/Footer}} | |
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Latest revision as of 18:45, 21 October 2009
[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]
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| Risk List | Tools and Documentation | Inception | Elaboration | Construction | Transition | |||||||||||||||||
| 1 | 2 | 1 | 2 | 1 | 2 | 3 | 1 | 2 | ||||||||||||||
| apr. 20 | may 18 | jun. 01 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | okt. 15 | ||||||||||
Basically anyone may change anything at any time for any reason, and the Configuration Manager keeps an eye on how (and how much) the Wiki and the SVN repository are used. He also writes this document (assisted by the Facility Manager(s) and others for lab-specific parts).
Tools, Environment, and Infrastructure
Modelling
Describe the computing environment and software tools to be used in fulfilling the CM functions throughout the project or product lifecycle. Describe the tools and procedures required used to version control configuration items generated throughout the project or product lifecycle. Issues involved in setting up the CM environment include:
- anticipated size of product data
- distribution of the product team
- physical location of servers and client machines
Most documents are created on the Wiki, which has built-in version control features (a revision history, including comments). For Google Docs the same is true. Our network drive does NOT have version control and should not be used for documents that have to be modified (much). For storing/exchanging Matlab code we will use [http://subversion.tigris.org/ Subversion] in combination with [http://code.google.com/ Google Code]. All team members wishing to alter models/write matlab code should follow the following steps to get set up (focusses on Windows):
- Download and install Matlab R2009a. (Login and click on My Account, both in the upper-right corner, then click on "My Products / Get Licensed Products and Updates".)
- Download and install TortoiseSVN: http://tortoisesvn.net/downloads
- Checkout the URL https://igemgroningen.googlecode.com/svn/trunk/ using TortoiseSVN by right-clicking in your iGEM directory (in Windows Explorer) and choosing SVN Checkout. Note that you will have to supply the password that can be found on http://code.google.com/hosting/settings.
Whenever you want to make changes to some of the files in the repository, first update all files by choosing SVN Update from the right-click menu in Windows Explorer (this will download any new changes from others), then make your changes, and finish by committing (again through the right-click menu). Do not forget to supply a commit message explaining the changes.
Also, in case of conflicts in a Simbiology project you are in trouble (this happens when two people update/change/commit a file at the same time). Unfortunately Mathworks chose to save their projects as one big compressed file, which makes it extremely hard to compare two versions of a project, let alone resolve conflicts. Using [http://winmerge.org/ WinMerge] (with the 7-Zip plugin) these project files can be compared, but you still can't resolve conflicts. So, please stick to one model per project and try to avoid conflicts. If a conflict does occur, contact Jasper for help in resolving it.
A list of programs that support SBML and there respective capabilities are here [http://sbml.org/SBML_Software_Guide]./SBML_Software_Matrix
Finally, team members that do NOT write code can checkout the models using TortoiseSVN in the same way as described above and file issues in the [http://code.google.com/p/igemgroningen/issues/list issue list].
Wet Work
- Tools:
- Ligation ratio: Cloning Tool 6.0 (ask Frans/Sven)
- List of used lab tools (and from whom we got them) can be found on GoogleDocs (in Dutch): Lab benodigdheden
- Environment:
- Lab room D113 in Haren
- Infrastructure:
- Archives: Binders for primer sheets, Articles on the subprojects
- Databases used are [http://openwetware.org/wiki/Main_Page OpenWetWare], [http://www.partsregistry.org/Main_Page Part], [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Groningen Sandbox],[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
Human Practice
A survey was made and executed. The consideration and results can be found here
Documentation
Identification Methods
Private files are stored in a central repository (currently the Y-drive or Google Docs). Agendas and minutes are stored in their respective folders under the date of the meeting in yyyy-mm-dd format to enable easy sorting. Other documents should be named according to the UPEDU standard as much as possible and prefixed by a short abbreviation in brackets (which makes it easy to reference them), for example [PP] for this document.
All documents that are not necessarily private should be placed on the Wiki under the name of the [http://www.upedu.org/upedu/process/artifact/ovu_arts.htm relevant artifact] (also see the [http://www.upedu.org/upedu/process/artifact/tmpl_cs/ovu_tmplcs.htm list of templates]), always prefixed by Team:Groningen (for example Team:Groningen/Vision). Images can also be uploaded to the Wiki to accompany texts, but the Wiki should not be used as a general means of exchanging files (for this the Y-drive, Google Docs or Google Groups are more suitable).
Finally note that any changes to documents on the Wiki should make use of the Summary field below the large edit text box to describe the change (it would be nice if you tick the "This is a minor edit" checkbox if you're making small tweaks, like correcting a spelling mistake). These descriptions can be long, or as short as one word, depending on the situation. Afterwards it should be possible to reasonably easily get an overview of how the document evolved, and to look up specific changes. For documents not on the Wiki a Revision History should be present at the top of the document.
Master of Lists
DONE: Anything about lab stuff (in green!)
- Our wiki
- Category:Team:Groningen contains all our categories (corresponding to some of the UPEDU disciplines).
- Category:Team:Groningen/Disciplines contains all our disciplines.
- Category:Team:Groningen/Roles contains all our roles.
- Team:Groningen is our main page, http://www.igemgroningen.com/ redirects to this.
- All our documents are on the Wiki, where possible. Each document is a subpage of the main page, unless it is itself part of another document, then it is a subpage of that document. For example: Team:Groningen/Project_Plan and Team:Groningen/Project_Plan/Risk_List.
- Note that each document should be preceded by a list of related categories (see this document for example).
- User:... (see, for example, Michael's user page)
- Some basic information
- Optionally a photograph
- Categories for each of the roles he/she has.
- Any JavaScript on the Wiki should (as much as possible/desirable) be written in a separate page and included using a script tag with a href attribute referencing the raw version of the page (see Template:Team:Groningen/Header for an example), this avoids problems with ampersands, keeps the pages a bit cleaner and makes it possible for browsers to cache long scripts. When it makes sense the page should be a subpage of the page it is used in.
- Parts list: List of glycerol stocks in -80 freezer C from MolGen, also the Quality control by PCR and Restriction analysis should be filled in here.
- Category:Team:Groningen contains all our categories (corresponding to some of the UPEDU disciplines).
- Subversion repository
- The trunk is at https://igemgroningen.googlecode.com/svn/trunk/
- /trunk/glucose/
- The models for the glucose sensing idea (which we're not pursuing any further).
- /trunk/buoyant/
- Models (mostly .sbproj files) for the buoyant bacteria.
- Google Docs
- Unfortunately Google Docs does not allow sharing of a directory structure.
- Contact Information for 3rd parties.
- Minutes and agendas.
- Availability of team members.
- Balance sheet: estimated costs for tickets, hotel, lab etc and estimated sponsoring.
- Primers: list with ordering date and concentration of the primers when they did arrive (also for oligo's).
- Chemicals / Materials taken from MolGen: list with all chemicals, materials, enzymes taken from MolGen
- Fridge/Freezer Stock list: list with different sheets for general stocks in the fridge and freeze, additionally a sheet for -20 freezer stocks of all labworkers.
- Lab tools: list of all the stuff (machines, pipettes, etc) we use from microbiology and practicum pool (Labbenodigdheden).
- Y-drive
- The transfer documents.
- Literature?
- Miscellaneous files
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