We've also been using a wiki as lab notebook for 2.5 years and it has stood the test of time. Since our aim is to make our data public we make extensive use of GoogleDocs, Flickr, YouTube, etc. A blog linking back to individual lab notebook pages on the wiki makes it easy to discuss higher level concepts while providing links to the fine details should anyone care to probe further.
Eric
· 1 year ago
Yeah; my workflow, I think, is significantly easier because I'm not writing the notebook for public consumption; it makes dealing with non-text data much easier by letting me keep most of that offline.
laura
· 1 year ago
first of all, only four posts in and already a cool blog - impressive :)
i'm starting my PhD and supervisor told me to keep a log of meetings i attend etc. which got me thinking i could as well open up another blog in which to post these things, instead of keeping a word file, eg in order to be able to incorporate links to stuff i looked up after a discussion. not sure how supervisor will feel about me writing about experiments or thoughts re projects, but might do it anyway, too.
anyway, sorry about the rant.
point is: do you think that keeping a blog as notebook is feasible? what would be the advantages of a wiki?
alf
· 1 year ago
What do you find are the advantages of using a wiki over something more blog-like such as Wordpress?
Alethea
· 1 year ago
I've been having the same thoughts. What you write about even wiki markup being problematic for some is true. Jean-Claude, I gave wikispaces a look and a definite advantage is the visual editor and ease of image upload. On the other hand, a definite advantage of the OWW platform is automatic entry creation by clicking on a date. What I haven't found in either is a way of retrieving chronologically ordered entries by tag (where I would then specify a "project" in the way JCB does by Experiment), but I know it could be possible. That would be pretty damn useful as we have a lot of different things going on, some of which crosses into two ostensibly separate projects.
GoogleDocs is perfect for what we need, JCB; thanks for putting me onto that. I knew about it but not that it was so easy to link out.
I'm still mulling over my list and priority order of desiderata but overall, I agree with your whole assessment, Eric.
I wanted to ask both of you (if JCB comes back for more) how you back up a wiki? I was wondering if I shouldn't just print out my entries once a month for my administration, who is quite reticent to have us move off paper as they've spent large amounts of money on serially numbered formal lab notebooks with room for countersignatures and the like. But that would stink wrt all the links, and the source is illegible.
Eric
· 1 year ago
It comes down to personal preference, I think. Each has there own advantages. A good blogging system can do almost everything a wiki can do, especially with the static pages that most platforms seem to support (such as Wordpress).
A blog is probably better for organizing entries by tags, categories, or chronology. With a wiki, you have to organize the chronology by hand; it's more flexible, but it's also not automatic. If you have a lot of entries, though, a blog probably becomes pretty unwieldy to browse through unless you have a really good search. I prefer organizing everything by hand, so that I can make it exactly the way I want it. Tags would be nice, but it's not a deal-breaker for me.
A blog would also be better for those who find editing wikis to be intimidating, since many of them have WYSIWYG interfaces; as Alethea mentioned, though, wikispaces is quite nice for those who have a hard time with the syntax, because the buttons and such are right there.
I like wikis, because I make a lot of really short entries over the course of a day, which would be a little bit more painful for a blog; it probably depends on your blog's visual layout, whether that would work for you. Not only that, but a wiki is helpful for working together in a lab, since the wiki can become a one-stop location for all the information in the lab. That would be a little harder to do with a blog.
Wikis are also better for keeping track of revisions and changes. A few blogs have that sort of ability, including Wordpress, but it's not as easy as with a wiki.
Really, I think it depends on the style and function you want out of a lab notebook.
As for backing up a wiki, it's the same as with backing up a blog. I usually make a dump of the backend database onto a hard drive; that's only for those who are comfortable with a command line, I'm afraid. In addition, the lab's wiki is on a university server, and the IT department has set up automatic backup of the entire server for every 2 hours.
I don't know if I'd print out wiki pages; if you're like me and you go back and add incremental notes to different pages, it would take forever (and lots of paper!) to print out all the pages with changes.
Ben
· 1 year ago
Laura, make it snarky, and let "anonymous visitors" comment :-)
Eric took the words right out of my mouth. Although it seems that blogs and Wiki's are increasingly converging in terms of functionality, I think it boils down to blogs being more single-person endeavors (in the sense that each entry hypothetically "belongs" to an author) while a Wiki is a more multi-person endeavor (in the sense that each entry is expected to be viewed and edited by multiple people).
And there is one other difference, although it's easily changeable, I detest how standard Wiki interfaces look. Search is a must-have feature, but someone really needs to teach people how to make better looking Wiki's...
Cameron Neylon
· 1 year ago
We use a blog as a lab notebook and Ben's comment is interesting as we definitely go for the 'one person - one blog' approach. We use a pretty fine grained approach to the organisation which I think is useful and have some automated stuff built in. We also tend to use OpenWetWare for actually sharing protocols and finalised things within the group.
Overall I think we get a bit hung up about blogs vs wikis. They are both fundamentally PHP running over SQL (or something similar). The differences are ones of expectation rather than underlying technology. I think its pretty clear the best system would take some of the strengths of both and put them together in a useful way. I would really like to look at the same underlying database in a 'wiki-view' and 'blog-view' to be honest - with each view bringing different things out.
Eric
· 1 year ago
I don't think wikis and blogs are the same technology. The fact that they both generate web pages from SQL data is what makes them possible choices for lab notebooks at all; that's kind of the bare minimum criterion for an online lab notebook in the first place, and thinking on that reductionistic level is just too coarse-grained to make useful judgment calls on what technology to use.
The interfaces of wikis and blogs are significantly different, and each is suited for a different style of content management. A wiki makes it easy to make a deeply-linked network of pages, while a blog makes it easy to create a set of chronologically ordered entries.
I do agree, though, that something that's sort of a hybrid would be nice...
Alethea
· 1 year ago
"I usually make a dump of the backend database onto a hard drive; that’s only for those who are comfortable with a command line, I’m afraid."
Could you point me in the direction of a tutorial? Even if my stuff is on OpenWetWare, I'd like to have a local copy in case they suddenly disappear (eg. if fascists get elected in November and decide to do completely away with free speech in Boston).
Seriously, it's a bit of a problem for me, as my blog is hosted by scienceboard.net which gives me WYSIWYG in exchange for my not having access to the actual database of entries, not being able to modify the look of the blog, not entering tracking codes or anything like that. With some WordPress functionalities nonetheless. Sigh. But Nature Network who kindly seduced me to write a blog with them, gives you about the same flexibility without WordPress, so not even WYSIWYG.
/rant
Eric
· 1 year ago
Here's a tutorial, but it requires access to the actual MySQL database server, which I'm not sure OWW would give you. The best thing is probably to talk to Bill Flanagan; he might be able to work something out with you.
Rory Macneil
· 1 year ago
We at Axiope will next week launch private beta testing of e-CAT, an OLN which has been specifically designed to enable non technical scientists to carry out experiments and manage data online. When our updated website goes live there will be a 'Links' section on the homepage where we link to interesting current discussions about online notebooks and related topics. I think this Moving Online thread is a good presentation of what is currently possible using wikis and blogs, and the issues with the two approaches. Would you have any objection if we linked to the thread on our homepage?
Thanks.
Rory
Rory Macneil
· 1 year ago
Sorry about that previous comment - number 14. It was posted in error. I would be grateful if you could remove it.
Thanks.
Eric
· 1 year ago
Sure, link it up, no problem.
Rory Macneil
· 1 year ago
Thanks, Eric, that's great. I will let you know when we go live.
Jean-Claude Bradley
· 1 year ago
As for back-ups, Wikispaces gives you the option of dumping the whole site into a zip file either as HTML or Wikitext at the click of a button.
The choice of blog or wiki depends a lot of what your requirements are. The ability to track versions is critical for us since an experiment can take some time to completely report and interpret.
Just like in a paper notebook, a table of contents is a small price to pay for quickly accessing experiments and easily done in a wiki.
The e-CAT beta went live this morning. There is a link to Moving Online on the revamped axiope.com homepage, where you can also watch the two introductory videos, and read about e-CAT's features, as well as the inaugural blog post to see a bit of the history and our aims for e-CAT. Feedback would be much appreciated!
All Comments
i'm starting my PhD and supervisor told me to keep a log of meetings i attend etc. which got me thinking i could as well open up another blog in which to post these things, instead of keeping a word file, eg in order to be able to incorporate links to stuff i looked up after a discussion. not sure how supervisor will feel about me writing about experiments or thoughts re projects, but might do it anyway, too.
anyway, sorry about the rant.
point is: do you think that keeping a blog as notebook is feasible? what would be the advantages of a wiki?
GoogleDocs is perfect for what we need, JCB; thanks for putting me onto that. I knew about it but not that it was so easy to link out.
I'm still mulling over my list and priority order of desiderata but overall, I agree with your whole assessment, Eric.
I wanted to ask both of you (if JCB comes back for more) how you back up a wiki? I was wondering if I shouldn't just print out my entries once a month for my administration, who is quite reticent to have us move off paper as they've spent large amounts of money on serially numbered formal lab notebooks with room for countersignatures and the like. But that would stink wrt all the links, and the source is illegible.
A blog is probably better for organizing entries by tags, categories, or chronology. With a wiki, you have to organize the chronology by hand; it's more flexible, but it's also not automatic. If you have a lot of entries, though, a blog probably becomes pretty unwieldy to browse through unless you have a really good search. I prefer organizing everything by hand, so that I can make it exactly the way I want it. Tags would be nice, but it's not a deal-breaker for me.
A blog would also be better for those who find editing wikis to be intimidating, since many of them have WYSIWYG interfaces; as Alethea mentioned, though, wikispaces is quite nice for those who have a hard time with the syntax, because the buttons and such are right there.
I like wikis, because I make a lot of really short entries over the course of a day, which would be a little bit more painful for a blog; it probably depends on your blog's visual layout, whether that would work for you. Not only that, but a wiki is helpful for working together in a lab, since the wiki can become a one-stop location for all the information in the lab. That would be a little harder to do with a blog.
Wikis are also better for keeping track of revisions and changes. A few blogs have that sort of ability, including Wordpress, but it's not as easy as with a wiki.
Really, I think it depends on the style and function you want out of a lab notebook.
As for backing up a wiki, it's the same as with backing up a blog. I usually make a dump of the backend database onto a hard drive; that's only for those who are comfortable with a command line, I'm afraid. In addition, the lab's wiki is on a university server, and the IT department has set up automatic backup of the entire server for every 2 hours.
I don't know if I'd print out wiki pages; if you're like me and you go back and add incremental notes to different pages, it would take forever (and lots of paper!) to print out all the pages with changes.
Eric took the words right out of my mouth. Although it seems that blogs and Wiki's are increasingly converging in terms of functionality, I think it boils down to blogs being more single-person endeavors (in the sense that each entry hypothetically "belongs" to an author) while a Wiki is a more multi-person endeavor (in the sense that each entry is expected to be viewed and edited by multiple people).
And there is one other difference, although it's easily changeable, I detest how standard Wiki interfaces look. Search is a must-have feature, but someone really needs to teach people how to make better looking Wiki's...
Overall I think we get a bit hung up about blogs vs wikis. They are both fundamentally PHP running over SQL (or something similar). The differences are ones of expectation rather than underlying technology. I think its pretty clear the best system would take some of the strengths of both and put them together in a useful way. I would really like to look at the same underlying database in a 'wiki-view' and 'blog-view' to be honest - with each view bringing different things out.
The interfaces of wikis and blogs are significantly different, and each is suited for a different style of content management. A wiki makes it easy to make a deeply-linked network of pages, while a blog makes it easy to create a set of chronologically ordered entries.
I do agree, though, that something that's sort of a hybrid would be nice...
Could you point me in the direction of a tutorial? Even if my stuff is on OpenWetWare, I'd like to have a local copy in case they suddenly disappear (eg. if fascists get elected in November and decide to do completely away with free speech in Boston).
Seriously, it's a bit of a problem for me, as my blog is hosted by scienceboard.net which gives me WYSIWYG in exchange for my not having access to the actual database of entries, not being able to modify the look of the blog, not entering tracking codes or anything like that. With some WordPress functionalities nonetheless. Sigh. But Nature Network who kindly seduced me to write a blog with them, gives you about the same flexibility without WordPress, so not even WYSIWYG.
/rant
Thanks.
Rory
Thanks.
The choice of blog or wiki depends a lot of what your requirements are. The ability to track versions is critical for us since an experiment can take some time to completely report and interpret.
Just like in a paper notebook, a table of contents is a small price to pay for quickly accessing experiments and easily done in a wiki.
For a quick look at some screenshots of what I am talking about see slides from my talk in Manchester yesterday:
http://www.slideshare.net/jcbradley/manchester-...