Biosensor - Notes (AWS)

• kinds of storage:
• cloud storage
• data storage

• the dataset that I worked for was: 21,7 GB
• my folder where I was doing calculations was 275 GB
• 378 GB is Gowanus data in Gowanus folder on our drive
• 5 TB is scratch disk on HPC for my account. And I think that might be sufficient.
• 10 TB (that would be great)
• minimum 1,5 TB

• From my understanding they are corresponding to different AWS services that we can buy. (It is weird because some of them have comment that they are “free”).
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Compute power: EC2 instances →



Is it for free?

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Cloud Object Storage S3 (I don’t think we need that)


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Cloud database: Aurora, RDS

• LAMP PCR has different temperatures for example, which was for me very interesting.

Portable Isothermal Amplification Devices

• Examples: Genie III, BioRanger, Axxin T16-ISO. (Probably they are expensive. Maybe they could be useful for us in the lab for tests/validation).
• Features: These devices are small, battery-powered, and designed specifically for isothermal amplification like LAMP. They allow for field deployment, making them ideal for point-of-care diagnostics or environmental monitoring, such as contaminant detection in soil.
• Advantages: Portability, fast results, easy-to-use interface, and minimal power requirements.

Heating Block-Based Systems

• Examples: Simple dry bath incubators with temperature control. (Does it make sense, are they portable ?)
• Features: These are more basic than specialized LAMP devices but can maintain a stable temperature necessary for isothermal reactions. They are low-cost and flexible, suitable for initial tests or prototyping LAMP reactions.
• Advantages: Cost-effective, widely available, and simple to use. However, they lack real-time monitoring capabilities.

Fluorescence Detection-Enabled Isothermal Devices

• Examples: Optigene Genie III, NEB’s WarmStart® LAMP Kit coupled with fluorescence detectors.
• Features: These instruments provide real-time fluorescence detection, allowing for immediate readout of results as amplification progresses. This can be essential for a biosensor application where rapid feedback is necessary.

NEB LAMP Primer Design Tool

https://www.neb.com/en-us/products/m1804-warmstart-colorimetric-lamp-2x-master-mix-with-udg (NEB WarmSTart x 500 reactions $1200)

• Advantages: Quantitative results in real-time, high sensitivity, and ideal for real-world applications in biosensing.

Smartphone-Based or Low-Cost Imaging Systems

• Examples: Smartphone adapters for fluorescence or colorimetric readouts. This solution is pretty promising, since it could be a phone application which helps interpret colorimetric test.
• Features: With the rise of mobile biosensing, some systems integrate smartphones to capture and analyze results. LAMP reactions often yield a color change or fluorescence signal, which can be detected and quantified using smartphone cameras and image analysis software.

• Advantages: Extremely portable, user-friendly, and cost-effective. Excellent for on-the-go field applications and ideal for low-resource settings.

Microfluidic and Lab-on-a-Chip Devices

• Examples: Custom microfluidic chips integrated with heaters and optical detection. (I have no idea if that could be a valid design for us. Could Lab-on-a-Chip be the end design for of the biosensoe)
• Features: These setups combine sample preparation, LAMP amplification, and detection on a single platform. They can be customized for specific targets, such as detecting heavy metals or microbial genes associated with pollutants.

• Advantages: High precision, automation capabilities, and minimal reagent use, enabling efficient and rapid analyses.
• Disadvantages: The dominancy of some chemical and physical effects on small scale, especially capillary forces, surface roughness, and the interference of construction materials on the reaction processes. Thus, the well-established behavior of chemical systems in conventional lab analyzers might become more complicated in LOCs., The geometric accuracy and precision in microfabrication is quite high, but still not comparable to precision engineering.

Colorimetric LAMP Detection Kits

• Examples: Commercial kits that use pH-sensitive dyes or turbidity to indicate successful amplification.
• Features: These kits rely on a color change (visible to the naked eye) when the target is amplified, often requiring minimal instrumentation other than a heat block.
• Advantages: Simple visual readout, low cost, and no need for advanced equipment—suitable for environmental field testing and initial biosensor development.