October 2022 | Science

Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

12:32 PM |

You mention Jupyter seems to be visualized as populated with endless little Python programs and graphs, maybe some tables, etc and not "maybe this maybe that" reasoning.

I notice for USA NIH R&D Jan 29 2023 is the deadline for a new requirement for grants to explain in considerable precision how results are shared.

Your example of maybe an embedded inventory control data base is interesting. Labelling, barcodes ( whatever ) and sample naming is pretty essential.

"Sharing" with people on site in your group, in the 'group' but in facilities at a distance, and explaining to 3rd parties trying to graft the new knowledge onto their projects are really, really different sorts of communication.

Probably your line item of control is accessible via some program like Python script or from a notebook.

So, does a project end up with a 'master' 'lab book' with all of them poured together, or what ?

Why do little programs instead of paragraphs of indecision end up in notebooks ? A: Notebooks feel more like personal assets than project line items...

I suggested to an insider ISO 900X would be a better credential for science then these little vows of happy talk. He said: "Too expensive", I disagree. but not all science could be written up in that form. Theres no single answer to the open questions, none at all... But there can still be incremental improvement..

The new requrement:
Beginning in January 2023, the Final NIH Policy for Data Management and Sharing (NOT-OD-21-013) will require researchers to include a data management and sharing (DMS) plan in funding applications. In preparation for the policy implementation, NIH has launched a Scientific Data Sharing Website.

Interesting stuff,

Daniel B. Kolis

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Re: [DIYbio] DIY Refrigerated Centrifuge

12:10 PM |

I used Pelitier coolers for fuel systems, not life science wet lab. the Peltier 3 layer stack was pinned to a manifold which ran perhaps at a duty cycle of 50% with maybe 0.3 G of vibration continuously. As in nominally expected to run perhaps 3 years without maintenance.. This chilled Methane maybe down 45 C. Note Pelitier cooling versus expended power is very quirky. Unlike compression chilling, its weirdly non-linear, when lightly loaded versus cell capacity, its efficient and worsens as it achieves higher loading... ex a multi layer stack will do a better job at fixed dissipation then a less or singular stack... just because the one considered is a area of a postage stamp, the same thermodynamics apply...

I see some alum or perhaps some better allow test tube holders and assoc charging stations. Creating a center of gravity for a load is by definition pretty simple..

Yet, actually creating anything repeatability usable is a non trivial process of trial and error. Obviously, the best way to achieve the goal a few times is go someplace else with the 'right' equipment and ... the goal is achieved.

But *if* it is easy to visualize the requirement is ongoing, especially if other temperature management requirements are achieved; ( handling simplified, lower RMS of unwanted delta T deviations, etc. ) It might be worth considering.

Managing temperature is a very very common industry requirement. Omage has a catalog the weight of a hand brick and a half with thousands of doo dads to do these things...

https://www.omega.ca/en/

50 ml seems a convenient mass to consider chilling with a rechargeable aka 'battery' one of fixture...

ther unwanted wiggle in the centrifuge is Omega V^2 so again the question of the reasonableness or not of the notion involves extreme specification of the goals, delta T's and G's, how long the new temp must be maintained, etc....

Also, if for instance the device is rechargable on a USB 5 V port probably it can squirt back the temperature encountered. That is, instead of being an improvisation, such a device can be a normalizing aspect of utility in the science of the process itself, possibly...

Regards,

Daniel B. Kolis

On Mon, Oct 31, 2022 at 12:44 PM John Griessen <john@industromatic.com> wrote:

On 10/23/22 10:26, Dan Kolis wrote:
> Ive had complete success with Peltier fixtures. this $5 semi moves 8 W and has a 8 by 15 mm face...

What was it like balancing the weight and attaching wires so they don't move on a centrifuge rotor?
The 9V battery seems large for centrifuges we usually think of. Are you using an old school centrifuge for 50 ml vials?

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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

10:05 AM |

On 10/26/22 11:27, Dan Kolis wrote:
> I sort of visualise a DIY movement as a leading edge of a broader base of practices generally. However, this corresp. has made me
> visualise a specific dichotomy. Its "DIY" somewhat equated to "loner" as opposed to formal science without exception sizable
> groups ? Certainly the rubber hits the road on a notebook most when one of two things happen:
>
> * Its lost.
> * Its shared.
>
>
> Leaving an embedded running program in Jupyter may be a slight distraction as opposed to a passive formula for the maker(s), but
> its pretty instructive. I am sure of ONE thing for sure in my humble, finite life: I would rather have; /*Anybody's
> place-mat doodles and notebooks rather then any formal publishing output*/ for any idea, whatsoever. That applies to patents or
> 'papers', anything. So I am in the wow ! _The notebook is magic camp_.

The sharing aspect is a main thing. So, that makes me think of a little database project for tracking your inventory of parts
called partkeepr, and a new rewrite called Limas: https://github.com/Lopo/Limas that is built with a toolset called Symfony.
It's changing, and not ready yet, but has been useful to people wanting to efficiently track myriad things and query the database
about them. Mostly what I find about query jupyter is running queries from jupyter, not on jupyter content.

Having a structure and queries possible is important. (Whether each content creator uses it or not.)
Searchability and structure makes finding a reason to collaborate easier.

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Re: [DIYbio] DIY Refrigerated Centrifuge

9:44 AM |

On 10/23/22 10:26, Dan Kolis wrote:
> Ive had complete success with Peltier fixtures. this $5 semi moves 8 W and has a 8 by 15 mm face...

What was it like balancing the weight and attaching wires so they don't move on a centrifuge rotor?
The 9V battery seems large for centrifuges we usually think of. Are you using an old school centrifuge for 50 ml vials?

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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

11:46 AM |

Thanks Dakota,

seems a product with a vast heap of features.

I think I will lean into Jupyter as the log subsystem with a way to add notes without struggle. How uncertainty is absorbed into notes is the central issue to me I think. My stuff expects the worker to be reasonably distracted and will try to absorb cause and effect of searches and genomic operations without any attention by the worker.

Since this product takes lot fo file 'formats' I think the minimal exports I plan or have implemented will enable the motovated worker to use this well.

I can't quite visualize how educational institutions andor 'other' ones look at costs, both instantaneously and ongoing. Any of the costs seem to be justifiable in the technical sense. but the cost per se is coupled to the commitment to really rely on it nearly indefinitely, really.

Im not yet ready to think this out but one Idea I have entertained is a sale of a few TerrByte HD which shows up completely ram jammed full of genomic data and search tools and any number of users can use it. for a one time cost, just the HD which is a linux system ready to plop into any computer.

The point is to avoid external DB for many things, for a few reasons like avoiding sneak peeks by other companies, speed, etc.

Paying people to think for infrastructure is expensive and delays ridden, the notion might be the variable facts are stored on a different system entirely. then periodically the entire system is replaced, some weekend in/out and the newer features and db are all there with no excuses, no installs, no new learning curve required, at all. Notebooks are a small but important part of the offering(s).

Regards,
Daniel B. Kolis

my ref: chW27a 27 Oct 2022

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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

10:25 AM |

This is the best ELN I've found. https://www.labarchives.com/

On Thu, Oct 27, 2022 at 12:22 PM 'Timothy Fallon' via DIYbio <diybio@googlegroups.com> wrote:

Hi folks,

Thanks for the continuing discussion on this. I participated in a seminar yesterday that was purporting the use of "Semantic Wikis", for electronic lab notebooks, and other types of data organization. It seemed quite promising, and indeed is not the "Microsoft" or typical solution.

I am still learning about the concept, but am sharing the link to the seminar recording, in case others might also find it insightful:
https://twitter.com/openneurosci/status/1585579923917373441

All the best,
-Tim

___________________________________
Timothy R. Fallon, PhD
NIH NRSA Postdoctoral Fellow - Moore Laboratory

Center for Marine Biotechnology and Biomedicine
Scripps Institution of Oceanography
University of California, San Diego

tfallon@ucsd.edu
Google Scholar publications and citations
Website: http://photocyte.github.io
Pronouns: (he/him/his)

** I may send emails at odd hours due to my own flexible schedule. I respect your working patterns and do not expect responses outside of your working hours. **

On Oct 26, 2022, at 10:27 AM, Dan Kolis <dankolis@gmail.com> wrote:

OneNote is fine if your in the Microsoft Ghetto. I've used it. It's a fine product. all this drivel: "Version 2.hsjsgj can only read Version fdfj if you have MS 10.6 or 11 or eat oatmeal, or have the Norwegian version... or: paid for for the PAYED-or-locked-out-399 version", etc. Is somewhere between distressing and amusing. Or the sadness of watching people realise, very, very slowly a spreadsheet is no way to consolidate most machine readable complicated ideas.

I sort of visualise a DIY movement as a leading edge of a broader base of practices generally. However, this corresp. has made me visualise a specific dichotomy. Its "DIY" somewhat equated to "loner" as opposed to formal science without exception sizable groups ? Certainly the rubber hits the road on a notebook most when one of two things happen:
Its lost.
Its shared.

Leaving an embedded running program in Jupyter may be a slight distraction as opposed to a passive formula for the maker(s), but its pretty instructive. I am sure of ONE thing for sure in my humble, finite life: I would rather have; Anybody's place-mat doodles and notebooks rather then any formal publishing output for any idea, whatsoever. That applies to patents or 'papers', anything. So I am in the wow ! The notebook is magic camp.

Maybe I visualize DIYers as more like moonlighters; that there daily roles are sciencey, or students of it anyway ( same thing from a content-of- head perspective, almost ).

Regards,
Daniel B. Kolis

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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

9:16 AM |

Hi folks,

Thanks for the continuing discussion on this. I participated in a seminar yesterday that was purporting the use of "Semantic Wikis", for electronic lab notebooks, and other types of data organization. It seemed quite promising, and indeed is not the "Microsoft" or typical solution.

I am still learning about the concept, but am sharing the link to the seminar recording, in case others might also find it insightful:

https://twitter.com/openneurosci/status/1585579923917373441

All the best,

-Tim

___________________________________

Timothy R. Fallon, PhD

NIH NRSA Postdoctoral Fellow - Moore Laboratory

Center for Marine Biotechnology and Biomedicine
Scripps Institution of Oceanography
University of California, San Diego

tfallon@ucsd.edu
Google Scholar publications and citations
Website: http://photocyte.github.io

Pronouns: (he/him/his)

** I may send emails at odd hours due to my own flexible schedule. I respect your working patterns and do not expect responses outside of your working hours. **

On Oct 26, 2022, at 10:27 AM, Dan Kolis <dankolis@gmail.com> wrote:

OneNote is fine if your in the Microsoft Ghetto. I've used it. It's a fine product. all this drivel: "Version 2.hsjsgj can only read Version fdfj if you have MS 10.6 or 11 or eat oatmeal, or have the Norwegian version... or: paid for for the PAYED-or-locked-out-399 version", etc. Is somewhere between distressing and amusing. Or the sadness of watching people realise, very, very slowly a spreadsheet is no way to consolidate most machine readable complicated ideas.

I sort of visualise a DIY movement as a leading edge of a broader base of practices generally. However, this corresp. has made me visualise a specific dichotomy. Its "DIY" somewhat equated to "loner" as opposed to formal science without exception sizable groups ? Certainly the rubber hits the road on a notebook most when one of two things happen:
Its lost.
Its shared.

Leaving an embedded running program in Jupyter may be a slight distraction as opposed to a passive formula for the maker(s), but its pretty instructive. I am sure of ONE thing for sure in my humble, finite life: I would rather have; Anybody's place-mat doodles and notebooks rather then any formal publishing output for any idea, whatsoever. That applies to patents or 'papers', anything. So I am in the wow ! The notebook is magic camp.

Maybe I visualize DIYers as more like moonlighters; that there daily roles are sciencey, or students of it anyway ( same thing from a content-of- head perspective, almost ).

Regards,
Daniel B. Kolis

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Re: [DIYbio] Opening IGEM WWW video 15 minutes and maybe a bit as it proceeeds 26 --> 28 Oct 2022

12:45 PM |

iGEM Russia is corruptive, non-inclusive, not for disabled people, non-competent country

ср, 26 окт. 2022 г. в 20:34, Dakota Hamill <dkotes@gmail.com>:

I still just want some access to parts to mess around with and learn...without having to form an academic based group with a PI and all that jazz.

On Wed, Oct 26, 2022 at 1:12 PM Dan Kolis <dankolis@gmail.com> wrote:

What is iGEM ?
The iGEM Foundation is an independent, non-profit organisation dedicated to the advancement of synthetic biology, education and competition, and the development of an open, collaborative, and cooperative community.

Video welcome by convener / Camera talent Traci :
https://www.youtube.com/watch?v=-jOr8CLyWRs

She says all of the event will be spooled out to WWW over a week or so. Previous video coverage(*) was unusually competent; really ideal. So there is a lot here to work with without being in Paris at this precise moment...

Not just happy talk here... sched and URL etc.

Organizational home WWW :
https://igem.org/

Thank you, Traci H. !!!

Maybe if / when you want or read up as this progresses, you could poke a message here ?

That would be spiffy.

Comme mentionné, tout est international, mais la France est le pays hôte de ce pass.
Merci. Vive la France !

(*) Two years back, do to you know what....

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Re: [DIYbio] Opening IGEM WWW video 15 minutes and maybe a bit as it proceeeds 26 --> 28 Oct 2022

10:33 AM |

I still just want some access to parts to mess around with and learn...without having to form an academic based group with a PI and all that jazz.

On Wed, Oct 26, 2022 at 1:12 PM Dan Kolis <dankolis@gmail.com> wrote:

What is iGEM ?
The iGEM Foundation is an independent, non-profit organisation dedicated to the advancement of synthetic biology, education and competition, and the development of an open, collaborative, and cooperative community.

Video welcome by convener / Camera talent Traci :
https://www.youtube.com/watch?v=-jOr8CLyWRs

She says all of the event will be spooled out to WWW over a week or so. Previous video coverage(*) was unusually competent; really ideal. So there is a lot here to work with without being in Paris at this precise moment...

Not just happy talk here... sched and URL etc.

Organizational home WWW :
https://igem.org/

Thank you, Traci H. !!!

Maybe if / when you want or read up as this progresses, you could poke a message here ?

That would be spiffy.

Comme mentionné, tout est international, mais la France est le pays hôte de ce pass.
Merci. Vive la France !

(*) Two years back, do to you know what....

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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

10:27 AM |

OneNote is fine if your in the Microsoft Ghetto. I've used it. It's a fine product. all this drivel: "Version 2.hsjsgj can only read Version fdfj if you have MS 10.6 or 11 or eat oatmeal, or have the Norwegian version... or: paid for for the PAYED-or-locked-out-399 version", etc. Is somewhere between distressing and amusing. Or the sadness of watching people realise, very, very slowly a spreadsheet is no way to consolidate most machine readable complicated ideas.

I sort of visualise a DIY movement as a leading edge of a broader base of practices generally. However, this corresp. has made me visualise a specific dichotomy. Its "DIY" somewhat equated to "loner" as opposed to formal science without exception sizable groups ? Certainly the rubber hits the road on a notebook most when one of two things happen:

Its lost.
Its shared.

Leaving an embedded running program in Jupyter may be a slight distraction as opposed to a passive formula for the maker(s), but its pretty instructive. I am sure of ONE thing for sure in my humble, finite life: I would rather have; Anybody's place-mat doodles and notebooks rather then any formal publishing output for any idea, whatsoever. That applies to patents or 'papers', anything. So I am in the wow ! The notebook is magic camp.

Maybe I visualize DIYers as more like moonlighters; that there daily roles are sciencey, or students of it anyway ( same thing from a content-of- head perspective, almost ).

Regards,

Daniel B. Kolis

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[DIYbio] Opening IGEM WWW video 15 minutes and maybe a bit as it proceeeds 26 --> 28 Oct 2022

10:02 AM |

What is iGEM ?

The iGEM Foundation is an independent, non-profit organisation dedicated to the advancement of synthetic biology, education and competition, and the development of an open, collaborative, and cooperative community.

Video welcome by convener / Camera talent Traci :

https://www.youtube.com/watch?v=-jOr8CLyWRs

She says all of the event will be spooled out to WWW over a week or so. Previous video coverage(*) was unusually competent; really ideal. So there is a lot here to work with without being in Paris at this precise moment...

Not just happy talk here... sched and URL etc.

Organizational home WWW :
https://igem.org/

Thank you, Traci H. !!!

Maybe if / when you want or read up as this progresses, you could poke a message here ?

That would be spiffy.

Comme mentionné, tout est international, mais la France est le pays hôte de ce pass.

Merci. Vive la France !

(*) Two years back, do to you know what....

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Re: [DIYbio] DIY Refrigerated Centrifuge

8:10 AM |

I did try this, rather than refrigerating the whole centrifuge just refrigerating the removable carousell (big lump of metal) , OK for a few short spins but the machine quickly heats it up. Some setups might allow you to add ice or dry ice to the tube carrier (obvs. be careful with dry ice and not popping gas tight things).

On Tuesday, October 25, 2022 at 4:59:25 AM UTC+1 Juul wrote:

Do be careful if deciding to cool the entire centrifuge. The centrifuges that have built-in cooling generally have at least some of the electronics encased in conformal coating to prevent issues with condensation. The small tabletop centrifuges I've taken apart don't have this feature. If your lab happens to have a dry air source (e.g. for IR spectrometry) then you could maybe do something with that to prevent condensation. If you are cooling the centrifuge itself then you likely want to add condensation protection and I don't recommend manually adding conformal coating to the circuit boards without also adding extra cooling for the mosfets since the mosfets in the three-phase inverter dissipate enough power that overheating is a common failure mode in the medium format eppendorf refrigerated centrifuges even though those are strapped to a block of aluminum which is then strapped to the thick steel case of the centrifuge chamber. Normally I'd be gung ho about people hacking their gear and seeing what breaks but I assume you don't want to risk killing your centrifuge with the difficulty of importing stuff into Sri Lanka right now.

On Sun, Oct 23, 2022 at 5:12 PM Jonathan Ferooz <atgs...@gmail.com> wrote:

Putting the centrifuge in a cool bag with cool pack? Or just putting the rotor in a fridge before?

Le 22/10/2022 à 19:59, Kavish Sirisena a écrit :

Greetings fellow researchers!

I am in need of a refrigerated centrifuge to process some proteins samples extracted from a mammalian cell line. The lab that I currently work does not have a refrigerated centrifuge to accommodate this. Is there any other alternative way to reduce the temperature of the working conditions?

I was thinkin maybe I could suspend a small eppendorf tube inside a bigger tube filled with water and subject it to freezing. However I am not sure how this would affect the centrifugation procedure.

Looking for your valued opinions on this matter!

TIA

Kavish
IRD Genetics - Sri Lanka
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Re: [DIYbio] Microgrants to document open biology workshop protocols

8:04 AM |

If anyone's interested we created an SOP system to support our registration for CL1 at London Biohackspace and have tried to keep it public on the githubs: https://github.com/london-biohackers/biohackspace-sops. Probably needs a bit of updating now but if anyone does do this work I'm happy to answer questions about it.

On Saturday, September 24, 2022 at 6:44:41 PM UTC+1 atgs...@gmail.com wrote:

Using DIYbiologists as a tool for the business... I'm sad and not agree at all.
Jonathan

Le ven. 23 sept. 2022 à 15:22, Thomas Landrain <thomas....@gmail.com> a écrit :

Hey folks,

It's been a while since I posted here. I would like to attract your attention to a micro grant program we are running at JOGL in partnership with iGEM to support the documentation of open and safe biology protocols.
You can obtain a 500 euros grant if you project is positively reviewed by the community :)

More information here:
https://app.jogl.io/peer-review/SOPbio1

Would love to see more DIYbio application in there!
Cheers
Thomas

—
Thomas LANDRAIN
Co-Founder & CEO, JOGL.io - Just One Giant Lab

We make Science and Innovation more inclusive, efficient, fun and impactful

Ambassador, iGEM Foundation

Former member, Conseil National du Numérique

Co-Founder & former CEO, PILI
Co-Founder & former CEO, La Paillasse

Book a meeting with me

Twitter: @Tholand_ @JustOneGiantLab @_PILIbio
Mobile: +33 678 37 31 36

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Re: [DIYbio] DIY Refrigerated Centrifuge

8:59 PM |

Do be careful if deciding to cool the entire centrifuge. The centrifuges that have built-in cooling generally have at least some of the electronics encased in conformal coating to prevent issues with condensation. The small tabletop centrifuges I've taken apart don't have this feature. If your lab happens to have a dry air source (e.g. for IR spectrometry) then you could maybe do something with that to prevent condensation. If you are cooling the centrifuge itself then you likely want to add condensation protection and I don't recommend manually adding conformal coating to the circuit boards without also adding extra cooling for the mosfets since the mosfets in the three-phase inverter dissipate enough power that overheating is a common failure mode in the medium format eppendorf refrigerated centrifuges even though those are strapped to a block of aluminum which is then strapped to the thick steel case of the centrifuge chamber. Normally I'd be gung ho about people hacking their gear and seeing what breaks but I assume you don't want to risk killing your centrifuge with the difficulty of importing stuff into Sri Lanka right now.

On Sun, Oct 23, 2022 at 5:12 PM Jonathan Ferooz <atgstart@gmail.com> wrote:

Putting the centrifuge in a cool bag with cool pack? Or just putting the rotor in a fridge before?

Le 22/10/2022 à 19:59, Kavish Sirisena a écrit :

Greetings fellow researchers!

I am in need of a refrigerated centrifuge to process some proteins samples extracted from a mammalian cell line. The lab that I currently work does not have a refrigerated centrifuge to accommodate this. Is there any other alternative way to reduce the temperature of the working conditions?

I was thinkin maybe I could suspend a small eppendorf tube inside a bigger tube filled with water and subject it to freezing. However I am not sure how this would affect the centrifugation procedure.

Looking for your valued opinions on this matter!

TIA

Kavish
IRD Genetics - Sri Lanka
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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

7:54 PM |

Hi Dan,

For most diybio folks I think OneNote would/might work great. If you need number crunching (biostatistics), then python/jupyter would be needed.

Personally, I have only been playing with diybio for the past year and wanted to start with something simple. I ended up developing an interest in replicating the biotech industries Nucleic Acid extraction technologies. So I really don't need anything more than something like Onenote.

Anthony

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From: diybio@googlegroups.com <diybio@googlegroups.com> on behalf of Dan Kolis <dankolis@gmail.com>
Sent: Monday, October 24, 2022 7:16:35 PM
To: DIYbio <diybio@googlegroups.com>
Subject: Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

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.

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:

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.

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

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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 settings

Thank 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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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

4:16 PM |

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.

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:

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.

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

Get Outlook for Android

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 settings

Thank 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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Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

11:42 AM |

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

Get Outlook for Android

From: diybio@googlegroups.com <diybio@googlegroups.com> on behalf of Dan Kolis <dankolis@gmail.com>
Sent: Monday, October 24, 2022 11:57:52 AM
To: DIYbio <diybio@googlegroups.com>
Subject: Re: [DIYbio] Electronic and other old fashioned lab notebooks in and out of formal settings

Thank 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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