online lab notebooks

[Andrew Barney]

Every once in awhile someone mentions the idea of documenting work in
online lab notebooks. What I'd like to know is, what are the best
options and are there any good examples?

Is the wiki style notebook listed by OpenWetWare the best one
available? http://openwetware.org/wiki/Lab_Notebook

In my case, I'd need one that is already hosted by someone else. I
have no way of hosting my own at this time. Perhaps the wiki style is
exactly what I'm looking for. Are there any others out there that are
optimized for diy science?

Thanks, this is all very new to me.

-Andrew

[Andrew Barney]

Has anyone here tried Evernote?

[cameron]

I use Evernote to clip things from webpages. Saving is easy and they
provide a feature that allows you to search across your evernote
content when you do a google search. Overall it is handy. However,
they force you continue logging in on a regular basis, which is
frustrating. I don't love the interface either. For this reason, I
find that I don't use it as often as I had hoped.
Cameron

[Ruediger Trojok]

Did you read the licence agreements of evernote? This is crap, open
source notes should not be posted there
Please especially note the point under e and f:


By submitting to Evernote any ideas, suggestions, documents and/or
proposals through the “Contact Us” interface or otherwise
(collectively, “Contributions”), you acknowledge and agree that: (a)
your Contributions do not contain confidential or proprietary
information; (b) Evernote is not under any obligation of
confidentiality, express or implied, with respect to the
Contributions; (c) Evernote shall be entitled to use or disclose (or
choose not to use or disclose) such Contributions for any purpose, in
any way, in any media worldwide; (d) Evernote may have something
similar to the Contributions already under consideration or in
development; (e) your Contributions automatically become the property
of Evernote without any obligation of Evernote to you; and (f) you are
not entitled to any accounting, compensation or reimbursement of any
kind from Evernote under any circumstances

[Derek]

I'm not a lawyer, but I believe that section pertains only to the
material submitted directly to Evernote through the "contact us" page.
The general terms of service state pretty clearly:

"Your Rights

As indicated above, you retain copyright and any other rights you
already hold in Content which you submit, post or display on or
through, the Service. Other than the limited license and other rights
you grant in these Terms of Service, Evernote acknowledges and agrees
that it obtains no right, title or interest from you (or your
licensors) under these Terms of Service in or to any Content that you
submit, post, store, transmit or display on, or through, the Service,
including any intellectual property rights which subsist in that
Content (whether those rights happen to be registered or not, and
wherever in the world those rights may exist). You agree that you are
solely responsible for protecting and enforcing those rights and that
Evernote has no obligation to do so on your behalf."

[Ruediger Trojok]

ok, thats true. But if you read further it still appears really
sketchy to me.
I have to admit that I do not totally understand what they are
precisely talking about at first glance,
it feels like they have the intention to take over your ideas:

5. PROPRIETARY RIGHTS, LICENSES AND LIMITATIONS

Evernote Rights
[...]

In order to enable Evernote to operate the Service, we must obtain
from you certain license and other rights to the Content you submit
(so that our processing, maintenance, storage, technical reproduction,
back-up and distribution, and related handling of your Content doesn’t
infringe applicable copyright and other laws). Accordingly, by using
the Service and posting Content, you grant Evernote a license to
display, perform and distribute your Content, and to modify and
reproduce such Content to enable Evernote to operate and promote the
Service. (You also agree that Evernote has the right to elect not to
accept, post, store, display, publish or transmit any Content in our
sole discretion.) You agree that these rights and licenses are royalty
free, irrevocable and worldwide, and include a right for Evernote to
make such Content available to, and pass these rights along to, others
with whom Evernote has contractual relationships related to the
provision of the Evernote Service, solely for the purpose of providing
such services, and to otherwise permit access to your Content to third
parties if Evernote determines such access is necessary to comply with
its legal obligations

[Atrus]

All it really means is that you allow evernote to hold the information, as any content you put is copyrighted, and they don't want you to sue them for infringing on your copyright.

It also says that you can't post copyrighted information of others without their permission.

It really doesn't seem all the strange and or over the top. Just lots of big words and 'cya'ing.

> I'm not a lawyer, but I believe that section p...

[Ruediger Trojok]

I do not see this so clearly from the text.
This is a private company that aims for profit. It is not open source.
They provide you a service that seems nice and shiny for free. How do
they get money out of it?
I do not really trust in this service, especially with such nebulous
terms of service.
A wiki system seems to be more appropriate and trustworthy to me.

On 1 Jan., 21:41, Atrus <atr...@gmail.com> wrote:
> All it really means is that you allow evernote to hold the information, as
> any content you put is copyrighted, and they don't want you to sue them for
> infringing on your copyright.
>
> It also says that you can't post copyrighted information of others without
> their permission.
>
> It really doesn't seem all the strange and or over the top. Just lots of big
> words and 'cya'ing.
>

[Jacob Shiach]

Evernote makes money by people upgrading to the premium subscription. Also, while evernote isn't open source, it should be noted that open source does not mean non-profit. There are a few profitable private companies that develop open source products.

**************
Jacob Shiach

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[Giovanni Lostumbo]

http://www.gnu.org/philosophy/who-does-that-server-really-serve.html
http://www.foaf-project.org/ (haven't been up to date on this one)
https://joindiaspora.com/
http://www.gnu.org/licenses/agpl.html
Really, the most free way to share and have complete control over one's data would be to keep it stored offline while having a client such as Status.net that allows you to choose what to share and replicate that on a wiki similar to what Diaspora could do, which is AGPL.
https://secure.wikimedia.org/wikipedia/en/wiki/Affero_General_Public_License
https://secure.wikimedia.org/wikipedia/en/wiki/List_of_AGPL_web_applications

[Giovanni Lostumbo]

Though, Openwetware seems quite open/free. I've been using it for more than a year. It's run using MediaWiki software, so it's possible that software has been rewritten for other websites with a user-interface that may be more custom to your needs, and that is most likely available if you contact that derivation. There are some free web domain hosting sites for charities http://www.knightsbridge.net/
http://knightsbridge.net/faq/index.html
I'm not sure if you can upload and run virtualized wiki software on there for zero cost, though, but maybe if you try! It would also be good for testing out to see what interfaces work well.

[Derek]

So Evernote and OpenWetware are being talked about as if they were in
the same space. They're really not. I mean, they can be used similarly
with public notebooks in Evernote, I guess, but that's really not it's
strength.

The main advantage I see to Evernote is that it makes the organization
of my personal notes on a variety of topics fairly easy. And those
notes are backed up and available online from any computer. And that's
about it.

If you don't trust Evernote then use google docs, or plain old text
files that you mail to yourself, or whatever other scheme you best use
to organize your thoughts. When you have something that you want to
share with the world compose it into a blog post, or a wiki entry, or
a journal paper or whatever format seems to communicate it best.

But the organization of my personal thoughts on a topic, and the
communication of some synthesis of those thoughts, seem like two very
different scenarios and to my eye Evernote really only excels at the
first. As such, I might use it for a lab notebook for myself (although
I tend to prefer paper for that) but by the time it gets cleaned up
for any form of public consumption Evernote would no longer be my
first choice for a shared format.

I like the wiki format (either on OpenWetware or any other wiki) for a
shared logbook. We used a wiki for our iGEM team the last couple of
years. But it's a logbook, not a lab notebook. My on-the-fly chicken
scratches wouldn't be very usable to others, so the logbook gets a
slightly higher level summary, although hopefully still at a low
enough level of detail to understand what went on in the lab. Trying
to write something for public consumption while in the middle of bench
work seems difficult, so I still need both.

Just my two cents...

--Derek

On Jan 1, 5:17 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>
wrote:

> Though, Openwetware seems quite open/free. I've been using it for more than
> a year. It's run using MediaWiki software, so it's possible that software
> has been rewritten for other websites with a user-interface that may be more
> custom to your needs, and that is most likely available if you contact that

> derivation. There are some free web domain hosting sites for charitieshttp://www.knightsbridge.net/http://knightsbridge.net/faq/index.html

> I'm not sure if you can upload and run virtualized wiki software on there
> for zero cost, though, but maybe if you try! It would also be good for
> testing out to see what interfaces work well.
>
> On Sat, Jan 1, 2011 at 3:42 PM, Giovanni Lostumbo <
>

> giovanni.lostu...@gmail.com> wrote:
> >http://www.gnu.org/philosophy/who-does-that-server-really-serve.html
> >http://www.foaf-project.org/(haven't been up to date on this one)

> >https://joindiaspora.com/
> >http://www.gnu.org/licenses/agpl.html
> > Really, the most free way to share and have complete control over one's
> > data would be to keep it stored offline while having a client such as
> > Status.net that allows you to choose what to share and replicate that on a
> > wiki similar to what Diaspora could do, which is AGPL.
>

> >https://secure.wikimedia.org/wikipedia/en/wiki/Affero_General_Public_...
>
> >https://secure.wikimedia.org/wikipedia/en/wiki/List_of_AGPL_web_appli...

>
> > On Sat, Jan 1, 2011 at 9:18 PM, Jacob Shiach <kingja...@gmail.com> wrote:
>
> >> Evernote makes money by people upgrading to the premium subscription.
> >> Also, while evernote isn't open source, it should be noted that open source
> >> does not mean non-profit. There are a few profitable private companies that
> >> develop open source products.
>
> >> **************
> >> Jacob Shiach
>

> >> On Jan 1, 2011, at 3:13 PM, Ruediger Trojok <ruedige...@googlemail.com>

> >> diybio+un...@googlegroups.com<diybio%2Bunsu...@googlegroups.com>
> >> .

> >> > For more options, visit this group at
> >>http://groups.google.com/group/diybio?hl=en.
>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "DIYbio" group.
> >> To post to this group, send email to diy...@googlegroups.com.
> >> To unsubscribe from this group, send email to

> >> diybio+un...@googlegroups.com<diybio%2Bunsu...@googlegroups.com>
> >> .

[Andrew Barney]

Thanks for the input everyone!

I haven't had a chance to try out the OpenWetWare wiki-style yet, but
concede it's probably the best all around option for sharing openly. I
look forward to testing it out and learning how the wiki formatting
stuff works.

I'm in the process of testing out Evernote. The main reason evernote
intrigued me was it looked like it had a simple interface, and it
boasted a feature that in essence used OCR software to index photos so
they could be searchable.

...The OCR software does seem to work, but the interface is slow and
clumsy, and does not present the search results as expected. Also,
I've already run out of my alloted monthly usage allowance for the
month, which puts a sour taste in my mouth. The free version kindof
sucks for anyone wanting to access it often, and i doubt the paid
version would be worth it.

-Andrew

> To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

[Paul Bartell]

Let me know what you are doing and stuff and as long as things aren't too high traffic and you dont use oodles of space, I can probably host wikis and stuff for free.

--
Random quote of the week/month/whenever i get to updating it: "Quis custodiet
ipsos custodes?": "who shall watch the watchers themselves?" - Juvenal

[Ruediger Trojok]

that sounds cool. How much space does a wiki need?
It should allow to include pictures. Video could be shared with the
help of youtube.
Is there a way to restrict access to certain areas in a wiki?
Lets say a couple of us are working on a project but do not wish to
have our shared wiki-notebook published immediatly,
so we work on it until it is in a presentable stage and then open
access for everyone...?

I also worked with a wiki for igem and have the same judgement about
it as Derek.
But I think the little to time consuming handling of an igem wiki for
benchwork
was also due to the high standard of a lab protocol igem required.
I could imagine more lax and easy ways of using such a wiki - for
simple brainstorming for example.
A wiki in general would be what we as a community could use best in
addition to this mailing list.
The list is outdated too quickly and discussions move on from one
topic to the next.
If there accumulates too much info, it is too messy to overlook, since
there is no proper order by topic.

Real work in progress would be better to digest with a wiki,
especially if we have international cooperations.

On 2 Jan., 07:08, Paul Bartell <paul.bart...@gmail.com> wrote:
> Let me know what you are doing and stuff and as long as things aren't too
> high traffic and you dont use oodles of space, I can probably host wikis and
> stuff for free.
>

> On Sat, Jan 1, 2011 at 10:01 PM, Andrew Barney <keen...@gmail.com> wrote:
> > Thanks for the input everyone!
>
> > I haven't had a chance to try out the OpenWetWare wiki-style yet, but
> > concede it's probably the best all around option for sharing openly. I
> > look forward to testing it out and learning how the wiki formatting
> > stuff works.
>
> > I'm in the process of testing out Evernote. The main reason evernote
> > intrigued me was it looked like it had a simple interface, and it
> > boasted a feature that in essence used OCR software to index photos so
> > they could be searchable.
>
> > ...The OCR software does seem to work, but the interface is slow and
> > clumsy, and does not present the search results as expected. Also,
> > I've already run out of my alloted monthly usage allowance for the
> > month, which puts a sour taste in my mouth. The free version kindof
> > sucks for anyone wanting to access it often, and i doubt the paid
> > version would be worth it.
>
> > -Andrew
>

> > >> >http://www.foaf-project.org/(haven'tbeen up to date on this one)

> > <diybio%2Bunsu...@googlegroups.com<diybio%252Buns...@googlegroups.com>

>
> > >> >> .
> > >> >> > For more options, visit this group at
> > >> >>http://groups.google.com/group/diybio?hl=en.
>
> > >> >> --
> > >> >> You received this message because you are subscribed to the Google
> > Groups
> > >> >> "DIYbio" group.
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> > >> >> To unsubscribe from this group, send email to
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> > <diybio%2Bunsu...@googlegroups.com<diybio%252Buns...@googlegroups.com>

>
> > >> >> .
> > >> >> For more options, visit this group at
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>
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>

> ...
>
> Erfahren Sie mehr »

[Giovanni Lostumbo]

"Is there a way to restrict access to certain areas in a wiki?
Lets say a couple of us are working on a project but do not wish to
have our shared wiki-notebook published immediatly,"

If there isn't a wiki out there that allows custom unlocking of
content, I would find one that allows the software to be run on your
computer. Then when you're ready to publish, either sync the wikis or
update the online mirror manually.

> > > >> >http://www.foaf-project.org/(haven'tbeenup to date on this one)

[James Clement]

I use Evernote. None of the ToS clauses discussed in this thread
appear sketchy, in my opinion. As stated by others, they are simply
protecting themselves from being sued, if they make backups or
distribute (to your own account) copies of your work from numerous
alternative servers. I've used the premium account for about a year
and love the fact that I can grab html, screen shots, pdfs., etc. and
upload to one account from my laptop, iPhone or iPad, and it will
quickly sync to any device I have.

Best regards,

James Clement, J.D., LL.M.

On Dec 30 2010, 5:27 pm, Andrew Barney <keen...@gmail.com> wrote:
> Has anyone here tried Evernote?
>

> On Tue, Dec 28, 2010 at 6:44 PM, Andrew Barney <keen...@gmail.com> wrote:
> > Every once in awhile someone mentions the idea of documenting work in
> > online lab notebooks. What I'd like to know is, what are the best
> > options and are there any good examples?
>
> > Is the wiki style notebook listed by OpenWetWare the best one

> > available?http://openwetware.org/wiki/Lab_Notebook

[John Griessen]

On 01/01/2011 10:35 AM, Ruediger Trojok wrote:
> Evernote to clip things from webpages. Saving is easy

Yes, the easy button!

"Accordingly, by using
the Service and posting Content, you grant Evernote a license to
display, perform and distribute your Content, and to modify and
reproduce such Content to enable Evernote to operate and promote the
Service. (You also agree that Evernote has the right to elect not to
accept, post, store, display, publish or transmit any Content in our
sole discretion.) "

They can rewrite it and not show it.

"You agree that these rights and licenses are royalty
free, irrevocable and worldwide, and include a right for Evernote to
make such Content available to, and pass these rights along to, others
with whom Evernote has contractual relationships related to the
provision of the Evernote Service, solely for the purpose of providing
such services, and to otherwise permit access to your Content to third
parties if Evernote determines such access is necessary to comply with
its legal obligations"

They seem to be saying that you are freepublishing if you put it on evernote.
and that they will modify your content if they want to, and tell the cops
whatever they want about what was withheld from public view. (Since the cops can
already see what is in public view.)

Seems simple and "Sure, and why not?" if you're freepublishing,
and avoid like the plague if you are
wanting a private service.

Status.net seems good for private notes for a group to use. I'm going
to install it on my server and see what it's like soon.

John

[John Griessen]

On 01/02/2011 10:16 AM, Ruediger Trojok wrote:
> Is there a way to restrict access to certain areas in a wiki?
> Lets say a couple of us are working on a project but do not wish to
> have our shared wiki-notebook published immediatly,
> so we work on it until it is in a presentable stage and then open
> access for everyone...?

This makes me think of content management systems,(CMS). I'm going to be trying one out
based on python language called django-cms. With django, a server hosting
users that can log in is easy -- they do not log into the server OS, they log into
the CMS. They can be limited in access privileges easily and probably there is
a way to quota them so they don't pull down the server.

A CMS combined with a wiki seems to be what you are asking for and it already exists:

http://taylanpince.com/blog/posts/django-doc-wiki/
https://github.com/sneeu/django-wiki
http://code.google.com/p/django-wikiapp/

JG

[Giovanni Lostumbo]

Also for CMS: Drupal http://drupal.org/

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[Giovanni Lostumbo]

Also, theres:

"Open Atrium is a GPL/BSD Drupal-based solution for collaborative project development with teams, etc."

"Open Atrium is an intranet in a box that has group spaces to allow different teams to have their own conversations. It comes with six features - a blog, a wiki, a calendar, a to do list, a shoutbox, and a dashboard to manage it all." http://openatrium.com/features

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[jcshieh]

OpenWetWare & wiki style seem useful if you want to share all your
results.

You could also use WordPress, Tumblr, or whatever blog service.

A few I looked into a while back (but not necessarily for publishing
out to the world - just to be able to search my lab notes better):

ORNL Electronic Lab notebook
http://www.csm.ornl.gov/~geist/java/applets/enote/
- I think it needs to be installed on a server but can handle whatever
you can put on a webpage

NoteBook - a Mac & iPad application
http://www.circusponies.com/

NotebookMaker - based on a FileMaker Pro database template
http://www.notebookmaker.com/

I just ended up keeping notes in a mishmash of Word docs & FileMaker
Pro database.

On Jan 3, 5:23 am, Giovanni Lostumbo <giovanni.lostu...@gmail.com>
wrote:

> Also, theres:
>
> "Open Atrium is a GPL/BSD Drupal-based solution for collaborative project
> development with teams, etc."
>
> "Open Atrium is an intranet in a box that has group spaces to allow
> different teams to have their own conversations. It comes with six features
> - a blog, a wiki, a calendar, a to do list, a shoutbox, and a dashboard to
> manage it all."http://openatrium.com/features
>

> > diybio+un...@googlegroups.com<diybio%2Bunsu...@googlegroups.com>
> > .

[Ruediger Trojok]

Hey people,
inspired by this discussion, and because I before felt the need to
document
some of the discussions we have here, I created a wiki for the
community
to set up long term projects.
The adress is
wiki.openbioprojects.net

It is brand new, so is is very virgin still. Help to populate it with
interesting stuff!
For example by transferring interesting and controversial topics from
this mailing list into the wiki.

Best, Rüdiger

On 6 Jan., 06:50, jcshieh <jcsh...@gmail.com> wrote:
> OpenWetWare & wiki style seem useful if you want to share all your
> results.
>
> You could also use WordPress, Tumblr, or whatever blog service.
>
> A few I looked into a while back (but not necessarily for publishing
> out to the world - just to be able to search my lab notes better):
>

> ORNL Electronic Lab notebookhttp://www.csm.ornl.gov/~geist/java/applets/enote/

> - I think it needs to be installed on a server but can handle whatever
> you can put on a webpage
>

> NoteBook - a Mac & iPad applicationhttp://www.circusponies.com/
>
> NotebookMaker - based on a FileMaker Pro database templatehttp://www.notebookmaker.com/

[Ruediger Trojok]

@jason bobe or whoever created the DIYbio logo:
I hope you agree on that I used it for the wiki, too.
If not please let me know.

[Bryan Bishop]

On Thu, Jan 6, 2011 at 7:26 AM, Ruediger Trojok wrote:

Help to populate it with
interesting stuff!
For example by transferring interesting and controversial topics from
this mailing list into the wiki.

or you can add it to the official DIYbio FAQ and wiki:
http://openwetware.org/wiki/DIYbio/FAQ
http://openwetware.org/wiki/DIYbio

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

[Giovanni Lostumbo]

http://p2pfoundation.net/?title=Jean-Claude_Bradley_on_Open_Notebook_Science&diff=46269&oldid=prev

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[Sachiko]

Hello, now 6 years later, there seems to be multiple options- do people have more experience? new recommendations?
is it still openwetware.org?

Thank you for any feedback.

s.

On Wednesday, December 29, 2010 at 2:44:58 AM UTC+1, Andrew Barney wrote:

Every once in awhile someone mentions the idea of documenting work in
online lab notebooks. What I'd like to know is, what are the best
options and are there any good examples?

Is the wiki style notebook listed by OpenWetWare the best one

available? http://openwetware.org/wiki/Lab_Notebook

[Bryan Jones]

I've just been trying out Benchling, seems pretty good so far.

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[Dennis Oleksyuk]

Yes, Benchling seems to be a really good tool for lab notebook, scheduling, and coordinating work between multiple people. It is also includes a number of tools for work with DNA sequences, plasmids, and primers.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAKw3Q70fTcYzyKgA8kKcCh0dxpSBgs5%2BFrow4AJ%3DeW%3D7KDXR6Q%40mail.gmail.com.

[Sebastian S Cocioba]

I'm still using Lab Guru. I really like it as an ELN. Always expanding weekly. Very good labels, inventory, etc. $100/year

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

[Koeng]

I find that evernote and a pen and paper notebook work the best for me. I use the rocketbook, which is a great notebook, to upload to evernote. I've found that I remember experiments better when using pen and paper, but still have search functionality of a written document.

-Koeng

[Dakota Hamill]

Just looked up rocketbook that looks sick.  Is it regular paper or plasticky?  Do all the pressure marks of writing multiple times remain?

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[Koeng]

Regular paper! The paper, in my naive view, is extremely good quality. Quite thick and the frixion pen works very well on it. I like the paper quality more than, say, moleskine's or some other notebooks I've tried.

Unfortunately, I haven't gotten a chance to try out the microwave function. The notebook lasts pretty long, especially if you take only about a page of notes a day. I'm only 3/4s through mine. For a limited time they sold a non-reusable version which I bought 5 of because I really like the paper though, so I guess it's not that big of a feature for me. 

From what I can tell with the Frixion erasable pens, only very minor marks will be made. It's also one of the only erasable pens I've found that isn't a novelty, it actually does writing and erasing quite well.  

-Koeng 

[Jake]

Might not be immediately apparent, but lab notebooks need to be in a bound composition notebook and written in permanent ink.  Notebooks that can have pages removed, or written with erasable utensils, cannot properly serve as a permanent record of your lab activities.  Just by using something like that you invite questions over the accuracy and completeness of your research notes.

[Simon Quellen Field]

In the old days, that was true, at least for legal purposes.

People got around those questions by sending mail to colleagues (or themselves) that are time-stamped by the post office.

But with something like Rocketbook, where the pages are shared to the cloud with date stamps, it is fairly easy to convince a judge of priority.

The easier we make it to actually take down the information, the more likely it is to be complete.

People who update their notebooks after a day's work might not remember to report everything.

Taking time-stamped photos (or videos) of the work is another way to help with completeness, and it even easier.

I'd bet a video of the researcher doing the work would make it easier to reproduce as well.

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[bostjan]

Hi!

Has anyone tried this app: http://scinote.net/ ?

Best wishes,

Boštjan

Dne sreda, 29. december 2010 02.44.58 UTC+1 je oseba Andrew Barney napisala: