Anyone know a good.spam free Wiki like Database for storing experiments and data?

[Josiah Zayner]

So with the launch of The Open Discovery Institute(ODIN) biohacking.DIYBIo store(http://the-odin.com) I also plan to relaunch The ILIAD Project(https://www.indiegogo.com/projects/help-identify-new-antibiotics-at-home-with-the-iliad-project).

The main problem I have been having is finding a suitable way for people to document their experiments. I play around with mediaWiki but the amount of spam was crazy! Even with custom editing of config files and installing modules I was having a difficult time keeping up with removing it all. Does anyone have any experience with any website templates or databases that use something similar to a wiki that would allow someone to document experiments they perform?


Thanks,
     Josiah Zayner, Ph.D.
     NASA Space Bioengineering Scientist
    

[leaking pen]

phpbb or other bulletin board system.   google docs. 

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[Josiah Zayner]

phpBB doesn't allow organization of data and is a forum not an editable database system. 

Is there a feature in Google Docs that allows the creation of something complex like a wiki?

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[Bryan Bishop]

On Fri, May 16, 2014 at 4:00 PM, Josiah Zayner <josiah...@gmail.com> wrote:

The main problem I have been having is finding a suitable way for people to document their experiments. I play around with mediaWiki but the amount of spam was crazy! Even with custom editing of config files and installing modules I was having a difficult time keeping up with removing it all. Does anyone have any experience with any website templates or databases that use something similar to a wiki that would allow someone to document experiments they perform?

I use git for version control and file storage, and ikiwiki for rendering for the web. Instead of using form fields in a browser to edit content, I just dump the files into the git repo and commit my changes. This gives me the option of storing whatever files I want, although I often stick with text-heavy files instead of binary blob file formats.

Here are some instructions I wrote up for how to "offline" edit an ikiwiki wiki, although the web interface also works:

http://diyhpl.us/wiki/

Another advantage is that the git repository is easy to clone to a variety of locations, there's a mirror over here:

https://github.com/kanzure/diyhpluswiki

There's a small application on top of ikiwiki, cgit, etc., that makes deployment much simpler (you can build the debian packages from source):

http://piny.be/piny-hosting/

So far nobody has been targetting ikiwiki wikis with git commit bot spam, but reverts are trivial and second (first?) nature with git. 

- Bryan
http://heybryan.org/
1 512 203 0507

[leaking pen]

wiki is a forum system with a good interlinking system.  it's NOT a database anymore than a bulletin board is.

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[Koeng]

subtiwiki makes you ask them (send the creator an email) to make an account and also tell why, prevents spam pretty well. Since they have to go through you, its pretty obvious which are spam and which are actual people. Perhaps try that.

[Josiah Zayner]

Yeah. Probably best way to go. Even though it sucks to need to personally verify every user.

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[John Griessen]

On 05/16/2014 04:48 PM, Josiah Zayner wrote:
> is a forum not an editable database system.

It's a big complexity leap and task, but there's
django framework for database driven web apps. Modules
in that framework exist for registering users that would lessen
the anti spam work, but not fully automate it.

For an anti spam shield against registering as a user were full auto,
it would be AI. We don't seem to be there yet.

Maybe that's why the subscription services are starting up.
The money pays for anti spam human verifying...

[Xabier Vázquez Campos]

I customised the Participants Database plugin for WP to make a database of primers and chemicals in the lab, and probably strains in the future. It is initially designed as database for people but works pretty well for us. You can add rich text fields, a security question now for submitting changes (we also had problems with bots),... fields are pretty easy to configure

[Josiah Zayner]

yeah...

I will just attempt to confirm the people manually. MediaWiki doesn't send an email when a new account request shows up which sucks. I guess I can attempt to fix that issue if I find the motivation.

Thanks all for the ideas everyone but I guess as most people said it is kind of unavoidable.

[Connor Dickie]

Hey Josiah,

You could check out www.synbiota.com - a fair amount of people/groups are using it to document, organize and share projects, protocols, data, etc.

Here's an example of a group that's using and enjoying it - https://www.synbiota.com/projects/455/

If you want to get a handle on the features available, best place to check right now are the short walk-throughs on youtube: https://youtube.com/synbiota

I'd be excited to hear feedback from you.

I'm pretty quiet on this group - but I just had to reply to your post. Seems as though you could save a lot of time using what we've built rather then rolling your own solution if I understand your requirements correctly.


! Caveat - I work at Synbiota, so FYI about that.


Regardless - hope you find a solution!

[Josiah Zayner]

Hey Connor,

   Is it possible to have multiple lab books connected to a project? If not that might be an interesting idea especially for collaborations. I actually don't even know what would be a good solution for something like The ILIAD project. How to make it easy for say 100 or 1000 people to collaborate and post experiments on a Science project? Do you feel that SynBiota would scale well? Just from a brief glance at the webpage you sent me it seems that it is more geared towards smaller collaborations? Maybe? I have been trying to use a Wiki because it seems that has been the most successful large scale collaboration tool but it was also built a while ago. A customizable front page to a Synbiota project might be cool also. I see one can edit the Details but those are hidden, one needs to expand that to see what is going on can that be changed by a project creator?

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[Katherine Gordon]

http://singularityhub.com/2014/05/17/aging-reversed-in-the-heart-brain-and-muscles-of-mice-thanks-to-blood-factor/

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[Mac Cowell]

The Public Lab for Open Science has a marvelous home-grown wiki (that supports markdown! Amen!) for enabling their community to collaborate and report on various experiments. Fork it!

https://github.com/publiclab/plots2

Mac

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[Josiah Zayner]

Thanks Mac. Checking it out.

http://singularityhub.com/2014/05/17/aging-reversed-in-the-heart-brain-and-muscles-of-mice-thanks-to-blood-factor/

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[Connor Dickie]

On Wednesday, May 28, 2014 11:08:21 AM UTC-4, Josiah Zayner wrote:

Hey Connor,

   Is it possible to have multiple lab books connected to a project? If not that might be an interesting idea especially for collaborations.

Interesting idea - Right now we don't have multiple lab books for a project. We encourage users to use tags and note types as a way to organize their data within a lab book. I guess you could say that we've organized things so that the users does not have to worry so much about organization. Search and metadata are key for us, especially as projects grow to have many participants (never though about thousands!), lots of entries, and lots of data.

One thing we do do is allow people to "branch" or "fork" (to use git parlance) lab books that have been listed under an open CC license. This is the method we're using for the #ScienceHack series of events where non-co-located groups are working towards a common goal and are building off of each other's results.

 

I actually don't even know what would be a good solution for something like The ILIAD project. How to make it easy for say 100 or 1000 people to collaborate and post experiments on a Science project? Do you feel that SynBiota would scale well? Just from a brief glance at the webpage you sent me it seems that it is more geared towards smaller collaborations? Maybe?

Some of the largest projects by team size are approaching 30 members as of now. A far cry from 1000, but we need to start somewhere and will not be able to determine what features and what affordances would allow us to scale projects from 1 person to 1000. We won't know what works for this until we encounter these scenarios. eg. we learned a lot when teams grew to be over about 12.
 

I have been trying to use a Wiki because it seems that has been the most successful large scale collaboration tool but it was also built a while ago. A customizable front page to a Synbiota project might be cool also. I see one can edit the Details but those are hidden, one needs to expand that to see what is going on can that be changed by a project creator?

This is being actively worked on, and you are not the first to request such features.

If you are keen - we work with many of our key users to help drive the design and features on Synbiota. I've followed your work since the kickstarter and would be excited to hear more of your requests, ideas and dreams about what an ideal software suite would be to you. I'm happy to connect via email or skype etc. to have a more in depth chat.

ronnoc[a]gmail[d]com

 

[John Griessen]

On 05/31/2014 10:30 AM, Connor Dickie wrote:
> One thing we do do is allow people to "branch" or "fork" (to use git parlance) lab books that have been listed under an open CC
> license.

Using version control could be useful as is to some people, but most researchers
would want some of git's complexity hidden in day to day use.
The terminology to describe notebooks could sound like:

Contribute and share an existing lab notebook, or start your own version?

Are you ready to publish results alongside others in the main project notebook?
Yes --> Which pages to publish? No--> What pages are ready for publishing in your notebook
to be called final, and what is still draft quality?
(Shows GUI for checking off status of pages, or selected text, etc.)

Some GUI menu choice for the notebook would show "all" including rough drafts, or final, hiding rough draft parts.

At individual contributor merge time, no interweaving of writings diagrams, photos,
data is done, it just becomes available for editing in the main notebook.
At publishing time those that have permission to edit it there
can merge into one cohesive document describing the work of all contributors together.

After individual contributor merges, changes to the separate individual contributor notebook would
trigger a merge reconciliation at any attempt to publish the current newer status of
work in the individual notebook. Merge reconciliation would require at-the-same-time
authorization of both the overall project leader and the individual, and would be like
software code merging -- not necessarily easy for some folks to do. It might not be automatable
to have new writings flow into the main document from the individual contrib notebook.

Probably the best way to handle merges by individual contribs is that they get the entire contents
of the main doc version control and the main notebook gets all their content also.
Then they have their version of it as a branch. They can set things so they only see their branch,
or they can work in the main notebook. When using the main notebook, they would add to their
project contrib dir, (see below).
Then the easiest way forward is to do all edits in the main notebook and abandon
the individual branch after the first "for publication" merge.

Some would want to share data before ready for publication. If it just went into
a contributor data part of the main notebook, with no parts referenced in the main
notebook, merging would be easy, and only require authorization of the contributor.
After using some of a contributor's writings and data in the main doc,
merging gets more difficult again, the same as when ready to publish.

I can see multiple contributors to a project being easy up until the overall writing
that pulls the project together is done, then it gets messy. To keep sharing progress easy,
building the idea of project contributor directories into a notebook makes sense to me.
Then merges of info to share require only an individual contributor's OK.

[Jonathan Cline]

On Friday, May 16, 2014 2:00:59 PM UTC-7, Josiah Zayner wrote:

 

The main problem I have been having is finding a suitable way for people to document their experiments.

Have you already tried openwetware.org ?  
 
I have not had any spam on my lab notebook pages there, and there are many templates already set up.

 
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