Timothy R. Fallon said:
> I personally use Onenote as my electronic laboratory notebook (ELN), which is
> fairly unstructured. It would be nice to have something with more structure
> (i.e. templates), and a very flexible API for plugging in workflows and other
> pieces of software.
Dan says:
One notes is definitely reasonably capable. Have you ever tried Jupyter ? When you wish for workflows suddenly this really busts out the urge to be some sort of groupware; ex shared on somebody elses WWW for instance.
> I think, for a long time there were concerns about having "signability" and
> "traceability" for patents, so commercial ELNs used in Pharma had to
> include those. But, from my understanding now, at least in the USA & much of
> the world, patents are "first to file", rather than "first to invent",
> so I'm not sure how relevant these patent-induced notebook requirements are
> anymore.
Treaty of Paris international patents slowly wiped out first to invent. https://www.intepat.com/blog/patent/paris-convention-vs-patent-cooperation-treaty-pros-and-cons/ Slowly the PCT addenda rto the Paris convention has wiped out 'who invented this ?" fights with bound notebooks.
> The Open Protocol (LabOP) language project,
> https://bioprotocols.github.io/labop/ , has been trying to come up with a way
> to describe biological protocols in software.
> A absolutely beautiful thing, would be if executing the protocol, also
> automatically put the results into your "electronic lab notebook", but we
> (LabOP) are a very long ways off from that I think.
> I think, for a long time there were concerns about having "signability" and
> "traceability" for patents, so commercial ELNs used in Pharma had to
> include those. But, from my understanding now, at least in the USA & much of
> the world, patents are "first to file", rather than "first to invent",
> so I'm not sure how relevant these patent-induced notebook requirements are
> anymore.
Treaty of Paris international patents slowly wiped out first to invent. https://www.intepat.com/blog/patent/paris-convention-vs-patent-cooperation-treaty-pros-and-cons/ Slowly the PCT addenda rto the Paris convention has wiped out 'who invented this ?" fights with bound notebooks.
> The Open Protocol (LabOP) language project,
> https://bioprotocols.github.io/labop/ , has been trying to come up with a way
> to describe biological protocols in software.
> A absolutely beautiful thing, would be if executing the protocol, also
> automatically put the results into your "electronic lab notebook", but we
> (LabOP) are a very long ways off from that I think.
A subsystem in a lap notebook for machine readable protocols is an obvious software component. Because its desirability is obvious does not make it easier to invent and make truly an asset in general.
Anthony said:
> I struggled with this some time back. I agree with Timothy and settled on MS
> Onenote. I use Mathematica Home Edition for visualization as I am an academic
> mathematician. I have used Python and the Jupyter system.
Dan says:
Anthony said:
> I struggled with this some time back. I agree with Timothy and settled on MS
> Onenote. I use Mathematica Home Edition for visualization as I am an academic
> mathematician. I have used Python and the Jupyter system.
Dan says:
Do you think between Jupyter and One note either is much better for life science notebooks ?
Do you think multiple user issues etc is the deal breaker ... Execution of code in Jupyter is pretty fancy. Wow.
Do you think multiple user issues etc is the deal breaker ... Execution of code in Jupyter is pretty fancy. Wow.
Regards,
Daniel B. Kolis
On Monday, October 24, 2022 at 2:54:51 PM UTC-4 adva...@gmail.com wrote:
I struggled with this some time back. I agree with Timothy and settled on MS Onenote. I use Mathematica Home Edition for visualization as I am an academic mathematician. I have used Python and the Jupyter system.
Anthony
From: diy...@googlegroups.com <diy...@googlegroups.com> on behalf of Dan Kolis <dank...@gmail.com>
Sent: Monday, October 24, 2022 11:57:52 AM
To: DIYbio <diy...@googlegroups.com>
Subject: Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settingsThank you for those line items. here are top level URLS and a one line summary from my peeking.
https://www.notion.so/
Workflow GUI 'who does what, when' group tool.
https://www.smartsheet.com/
Nested PERT charts as orthag. speadsheets.
https://www.claris.com/filemaker/
Database add in tool, report generator.
I note { Pfizer-BioNTech or Moderna } spend > 1 Billion USF to get a mRNA vax shippable. Yet the essence of why there stuff was approached and AstraZeneca flopped would occupy maybe 6 printed page faces. Not opening the box of XX Billions in annual sales ... I think a notebook system scalable from free for students to supporting projects like this needs to grasp FDA sorta-kinda-traceability and where the files live matters greatly to decision makers.
Enabling both open ended research and "Do it because the boss says its right" is probably too much scope of work in a single IDE, but the underlying struct of knowledge might do this. I specifically 'diss the SAS model some lovely people who dont charge much or are free ( ex ad supported ) can be trusted with content. including all sorts of black hats. Jupyter has this utility... ipyng could live in highly secure boxes.. And starts free with no rules up to locked down like Nat. security is an interesting scope of work.
Interest in this is expanding. I note you cant send DNA clips via FB, I was corresp with a fine guy and tried and it bounced. was RNA, detected with there s/w and a polite note sent back and message suppressed. Don't try it if you don't want to endure annoyances... So maybe lab notebooks esp merged with real time people hookups will encounted this security in depth idea, too... Of course some shared notebooks might automatically obfusticate DNA sequences and conf of Atoms like PDBs, etc so the shared recip would be denied some of the copy and paste of it entirely... But still get the higher level goals. presumably they could ask for more as required.... One thing about a paper book is it can be poked int a vault. Of course it can also be photocopied.
Im not trying to proposed to write one. I am proposing to avoid doing that but interface unusually well with one. Thermo Fischer has a nice one, kind of expensive but not terriblly so ( $ 1K / user seat per year )... A wrapper around Jupyter seems a possibility.
Regards,Daniel B. Kolis
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