OpenWetWare:Ideas
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Wiki Changes incorporating SyntheticBiology.org and multiple entry pages
- that we rename the front page of the wiki (i.e., "endipedia")... by getting rid of the front page of the wiki
- that we have one wiki which serves endy lab, tk lab, and our synthetic biology working group.
- that the endy lab web page move in its entirety into a wiki-format, and that http://mit.edu/endy point to an internal wiki sub-page that is the new "endipedia."
- that the TK folks consider constructing a TiKipedia for the TK lab and that there be an internal wiki sub-page that is the TiKipedia port of entry.
- that the syntheticbiology.org website point to an internal wiki sub-page that is the new syntheticipedia, and that we move all information now on that website into wiki-format -- that site has gotten really stale, even though we are doing a lot more work.
- that a new URL (www.stinkjet.org) point to a still different internal wiki page that we can use to promote discussions of issues related to the development of second generation biological technology.
(emailed out by Drew 6/9/05)
- I think that one of the major advantages of the wiki as it stands now is the centralized nature of the technical information. By having having a single wiki page devoted to say "Ligations", everyone can contribute and place information about debugging problematic experiments in one place for the benefit of others. If we had separate ligation pages for the Endy, TK lab and Synthetic Biology then the barrier is raised to ongoing discussions between people about protocols. Therefore, if we do decide to change the wiki organization I would vote for maintaining a centralized place for technical information for all three groups. We can still eliminate the Main Page just by creating a new technical information front page that is linked off of all three groups.
- I prefer sbpedia to syntheticipedia.
- What is the difference between the synthetic biology wiki and a wiki about development of second generation biological technology? Shouldn't the latter be a part of the former?
- --Reshma 09:41, 10 Jun 2005 (EDT)
Communicating Changes to the Wiki
This has come up a couple of times. For those who check changes to the Wiki more frequently than checking for updates to \. I don't think its a problem. But it might be good to find a way to easily communicate changes to the wiki to all (who is all?). Possible ideas include -
- Just mail the endylab and tklab when you put up something. Easy but not very streamlined.
- Get the wiki to automatically send daily/weekly updates of non-minor changes to a mailing list of interested parties. Not sure if this is possible. Actually looks like enotif will do this, its a plugin for mediawiki. You choose to receive emails or not and which pages you want to be alerted to changes in. --BC 16:25, 26 May 2005 (EDT)
- Might be possible to automatically keep a recent updates section on the main page.
- Have everyone install RSS readers and subscribe to the RSS feed. Maybe a bit OTT!
Feedback?
--BC 16:15, 26 May 2005 (EDT)
Synthetic Biology Community on DSpace
I posted this below under Presentations/posters/papers but then thought it might not be very noticeable so I am reposting it with its own heading. It is a page about creating a Synthetic Biology community on DSpace which would enable us to post all digital materials produced by the group online and determine who gets access to them. Feedback much appreciated (you can also email me if you don't want to post on the wiki). --Reshma 15:54, 26 May 2005 (EDT)
User Wikis
Barry and I thought it might be cool to do an experiment evaluating "personal" wikis as a data organization tool. Similar to the local file structure that you would have in your computer home directory, but with better linking between sections and more transparent content. i.e. Not just word files in sub folders that I can't readily search or link between. (yes sri, i know spotlight can search them, but you still can't link easily)
I also think that if lab members format more of their personal remarks, etc, in wiki format they will be much more likely to make their way into the public wiki space. So will see how this works out. Of course this could all be done within the user pages on the current wiki, but i think there is some value to being able to take personal notes that aren't public domain. (but which eventually can move there easily).
Thoughts? Also, if you want to try it out for yourself we can set that up. Jasonk 14:41, 26 May 2005 (EDT)
- -Mac Users: if you want an easy walk through on how to set up your own wiki, go here. Takes about 30mins and sets up an Apache Web Server, a SQLl database, PHP and mediawiki. And its all OSS also! --BC 16:19, 26 May 2005 (EDT)
- -This seems like an interesting idea. One thing I am wondering is say I have a personal wiki and document a project on my personal wiki. How easy would it be for me, in the future, to move my wiki pages onto the lab wiki? Especially if I only want to move a section of my wiki to the lab wiki. If it is difficult to do this then it reduces the likelihood that people will eventually release their personal wiki pages to the public domain. Personal wikis might still be useful for the person but perhaps less useful as the documentation of a project that eventually gets released to the world. --Reshma 13:14, 27 May 2005 (EDT)
- -My thought on this is that right now if i had a project that i didn't want on the public wiki i would be documenting it on a word file on my personal computer anyway. So using a personal wiki instead just means that the formatting is already in place to just cut and paste to the public wiki when/if i'm ready to do that. So there may be a little work in moving it over (i.e. there's not just a "merge" button), but it should be less work then if i had just made a word file.Jasonk 15:31, 29 May 2005 (EDT)
- -This raises one of a few drawbacks to the personal wiki idea. The others are the difficulty of making a well ordered hard copy of your material, and embedding files is more cumbersome than when using Word or something equivalent. The merging of wikis problem might be partially solved by using a similar structure for a personal wiki as for the lab wiki and using the same list of categories, which would automatically integrate your pages into the lab wiki. For that to work, we'd need to rely on categories more than we do now. I'd be interested to hear from someone who knows about SQL databases and how easy it might be too merge two databases or portions of one database with another. I liked the personal wiki idea just as a way to organize my own material and make it easier to cut and paste individual pages to the lab wiki if I wanted. I think this would be really useful when developing a new protocol, it could live on a personal wiki until it works and then get moved over to the lab wiki. Time will tell though if it is ueful. --BC 15:37, 27 May 2005 (EDT)
Categories
I think we could use the Categories feature of the wiki more effectively. Having a list called Protocols and a category called Protocols seems redundant. What about using Categories to connect group pages across lists? For instance, a "Running systems in a μreactor" category could include links to ordering microfluidics (under Protocols), the Scope (under Equipment), media (under Materials) and other relevant pages. This approach would essentially use Lists and Categories as two separate "dimensions" along which pages can be grouped. --Reshma 21:13, 25 May 2005 (EDT)
- Yeah that's good -- I like the idea of grouping things from multiple lists in relevant ways, the question is when do categories become more useful then just creating a "Running systems in a μreactor" page and then linking to everything like that? For instance take the media (or the scope), how many categories could it end up being in? running a μreactor, running a macro chemostat, growing a batch culture, etc. In that case I think having seperate "group pages" or something that each individually pointed to the media might be better. Jasonk 00:55, 26 May 2005 (EDT)
- I think the categories might pay off better if we had a lot of protocols that were distributed accross different heirarchical list schemes. For instance if I started adding new protocols to my user page directly, in some sort of heirarchy that was relevant to me, i.e. "frequently used protocols" vs. "infrequently used protocols" or something, then I could just slap a category tag at the end and know that I had placed it into an appropriate spot in the aggregate general protocol area. Also, could imagine if you aggregated a few lab wikis together that had pre-defined heirarchies, the categories could serve to create a common protocol space without everyone having to conform to the same list scheme. So it might be that they are more useful down the line (or not), but it certainly doesn't hurt to give any system a try and see if it proves useful (can always change it easily). Jasonk 00:55, 26 May 2005 (EDT)
I guess i'd like to think about what other categories would be useful.
Lab Notebook
Not planning on throwing my lab notebook online just yet, but if you were to consider using the wiki for such a thing you might want to have some sort of encrypted date/user signature. This would potentially give the more paranoid among us more ammunition in their attempt at defaming the person who "scooped" them in this guerilla war we call academics. (sarcasm tags would also be nice) Jasonk 18:27, 23 May 2005 (EDT)
Some relevant links:(thanks ilya)
- Open Source Electronic Lab Notebook Software
- Also, the pharmaceutical industry has some pretty serious electronic signature rules, which are patent-safe. Expensive to implement and likely overkill for academia but:
Suggested new name: knendipedia
- I think knendipedia might be a more appropriate name for this wiki :). (I liked knendipedia better than enightipedia). What do you think? -Reshma 10:07, 11 May 2005 (EDT)
- Maybe we should just go with something like SynthBioWiki or something, would make it easier to add more friends down the line, not sure the knendipedia approach scales, shetkoscanknendipedia :) Jasonk 18:26, 23 May 2005 (EDT)
- How about SBpedia - pronounced speedia --BC 19:33, 23 May 2005 (EDT)
- My one problem with the above two suggestions is that not everyone does 'synthetic biology' ie me, francios, jeff, ty, heather... --Sri Kosuri 23:29, 25 May 2005 (EDT)
- good point, then how about some generic bio term, like geneipedia, or some such nonsense.Jasonk 00:53, 26 May 2005 (EDT)
- My one problem with the above two suggestions is that not everyone does 'synthetic biology' ie me, francios, jeff, ty, heather... --Sri Kosuri 23:29, 25 May 2005 (EDT)
User page / posting personal ideas
It would be nice to post pages which are non-editable for things like your personal opinion on something scientific. I.e. the type of stuff that might be found on your user page. This also becomes more important if we open the wiki to be world-writable.
We could accomplish this by making all users admistrators since admins have ability to "protect" pages and lock them from editing. This would work so long as members were all trusted, but if we decide to expand member base we might like to have a way of doing it without giving everyone admin access.
Anyone know of how to do it without giving admin access?
Presentations/posters/papers
One thing that struck me as potentially useful would be a place to archive presentations and posters. Might be useful to be able to look over others presentations to see how they presented things etc. Similarly, it might be nice to also be able to post works in progress like papers or various writeups etc. Of course, I can imagine several levels of release like private (probably wouldn't post), release to the Knight/Endy lab (wiki?) and release to the world (http://www.syntheticbiology.org?).
- Does the wiki have a good mechanism for posting documents? A quick look suggested to me that you could only upload pictures.
- i think you can only do pictures, best bet for docs seems to be store elsewhere and link - i like the idea of having a place on model where we can dump all wiki docs/ppts/etc in a centralized place.Jasonk 14:40, 28 Apr 2005 (EDT)
- Can now post whatever type of file you like Jasonk 18:30, 23 May 2005 (EDT)
- Can sections of the wiki be made off limits to those without user accounts. ie non-readable?
- Or alternatively people can post documents in their own public directories. Use MIT's certificate system to control who access the directories and then just put an external link on the wiki. This gives maximum control over access to the author but does not centralize documents as much. This also may be problematic as people graduate or leave the lab.
- This is a good idea for now. In the future, we could create a section on model to have a username and login for private files. --Skosuri 14:36, 28 Apr 2005 (EDT)
- Any better ideas?
Collaborators
Forgot to mention in lab meeting, but will be giving the Knight lab write access to the pages, talked with reshma and austin and they thought it made more sense to just have one wiki we could share rather than cross referencing seperate wikis. (might need a new name then).
Also, we could consider starting Collaborative Projects pages, for things such as the Standard BB strain, etc.
Ideas from Lab Meeting 4/27
Openness of the wiki
Options for public access:
- World-writable and readable
- World-readable only
- World-no access
- Hybrid
- World can write to discussion but not to main articles.
We decided that we should go with option 2 for the time being at least until the wiki stabilizes and then consider making the wiki world-writable.
