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Order lab reagents using study protocols

Image credit: National Cancer Institute/Unsplash

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Jamila
Jamila Oct 16, 2020
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Instead of individually selecting laboratory reagents, could we use pre-existing laboratory protocols to help fill our shopping baskets?

So in this idea, you would use an author's name and/or study title to find reagents for your experiments. You'll search for the study in the search bar. Then you would click on the appropriate study protocol for your experiment. The system will suggest certain reagents to you based on the protocol you have chosen. Then you can start adding the reagents to your basket.

An example
You want to do an immunostaining technique, but you'd like to follow a certain author's study protocol.
  1. You put the author's name/study title into the search bar.
  2. The methods used in the study will come up in the search, and then you'll click 'immunostaining.'
  3. This will open up a page that tells you the kind of things you need. For immunostaining, you'll need a fixing reagent, blocking buffer, antibodies, counterstain, etc.
  4. After you click on 'blocking buffer,' the website will show you all the options available for blocking buffers.
  5. Then you can add your reagents.



This way, you can align your experiment with a previous protocol on the internet. You can also improve the pre-existing protocol because the shopping basket will be customisable.

Hopefully, we won't be forgetting reagents with this new technique too.

Any thoughts on the idea? Do you have any improvements?
1
Creative contributions

Extend the idea to create a modular laboratory management system for biological sciences

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Subash Chapagain
Subash Chapagain Jul 05, 2022
How about going a bit further and designing a lab management software that uses both the in-house and online databases to create optimized protocols for biological research? Most of the work we do as biological researchers overlap. Some of the key techniques used, for example, PCR, Cell cultures, RNA/DNA extraction, and Western Blots, are used ubiquitously irrespective of whether the lab is working on bacteria or viruses or any other pathogens (of course, with their own adaptation). Hence, to cut the time wasted adapting, could we use a lab protocol designing system that takes specific inputs and gives options based on these inputs for the reagents to use, where to order them from, along with other laboratory protocols for relevant assays and experiments?
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General comments

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Shireesh Apte
Shireesh Apte2 years ago
I like the idea but it is not really solving a problem. Reachers typically have registered vendor websites that they visit. I think it is easier to visit a known vendor site and just plug in the reagents etc. from a particular author's paper (which should be described in the "materials and methods" section; instead of trying to build a whole new platform for (what I consider to be ) a rather niche application.
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Shubhankar Kulkarni
Shubhankar Kulkarni2 years ago
Shireesh Apte I think the idea is not so much about the method of ordering the reagents as it is about identifying what exactly to order. Publications do not describe the methods in detail, and the commonly used ingredients are not listed. This platform will help those researchers with little previous experience in lab research. The platform will also tell you the intricate details of performing a particular experiment more efficiently, quickly, to obtain better results (better western blot quality, better DNA purity on isolation, etc, which are developed through experience and are not present in any laboratory-related books. It is similar to food recipes and identifying the appropriate ingredients to order. Also, as mentioned in another comment below, this solves the major problem of non-reproducibility. If a certain research group is unsuccessful with a certain experiment, they could also borrow the reagents, kits, and even cell lines from the lab that as successfully published their results.
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jnikola
jnikola3 years ago
Seems really great! I agree with everything mentioned and it would also make the process of introducing a new method to a lab much much easier. The problem that could arise is when the lab uses custom-made buffers or solutions (usually to save money, or to enhance the method; e.g. 97% EtOH instead of 70% in the RNA extraction).
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Shubhankar Kulkarni
Shubhankar Kulkarni3 years ago
Juran K. Since everything will be documented and open source (anybody can view), it will easier to identify fault and fraud.
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Shubhankar Kulkarni
Shubhankar Kulkarni3 years ago
I like the idea! The biggest problem it solves is that of reproducibility. I have read several times in publications that the authors could not reproduce the results probably due to the use of different reagents/ materials. If we have such a database, people can just look up the make and the company and order that reagent. This should also work for cell lines. The genotype of the cells varies with the passage number and that may, too, decrease the reproducibility. I would also like to see an option of transfer of biomaterials via the platform. For example, if a lab has a certain cell line and the experiment seems to work using those cells, another lab can procure the cells. Also, if a lab has extracted "tons" of a particular protein and does not need it anymore, they can ship it off to those in need.

It will also be helpful in tracking down the problems with reproducibility. If two labs use the same reagents but get different results, the problem can also be due to the batch variation of the reagents.

This idea can be coupled with the publication of research. Every paper has a "materials and methods" section. Instead of just writing the materials there, the authors should also add those to this database. That way, everything that goes into that particular research, is also available with the details.
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