Imaging. Data Mining. Writing. Devices.




Experiencing the pleasure of finding things out

Thursday, 12 January 2017 22:27

Compendium of open source biological software

This is just a short note that if you do any biological data analysis – whether it is sequence data, flow cytometry data or any other data then first look at Bioconductor website. This has open source data, mostly written in R, that enable you to see what is the process that is used to analyze the data as well as giving you the solution that enables you to do data analysis for the cost of processing time. There are many packages for genome sequence analysis and bioinformatics but there are interesting packages too. For example "imageHTS" for microscopy HTS data : Analysis of high-throughput microscopy-based screens.

Most of these packages run on the local machine but it is also possible to run them in the cloud based on your setup.

What is your favorite package in Bioconductor?

Sound as we listen is made up of multiple frequencies. The typical way of separating them has been computationally using an algorithm called a Fourier transform. However, researchers in Switzerland have managed to split sound into different frequency by way of a device – a 40cm aluminum case with 10 holes on its sides – almost like a recorder or a flute. The inner area is divided into chambers separated by a membrane that impedes a few frequencies.

The interesting application of this device could be to non-electrically isolate a specific frequency or make an "antenna" like device that would selectively listen to only one band of frequencies. This would be important in problem detection within machinery or other applications like that...

Any other application?

Monday, 09 January 2017 14:23

A very sensitive vibration sensor

Vibration sensing is important for sensing failure of instrumentation or found sound and vibration measurements. Technology for detecting sound has existed for a long time and usually employs a variety of microphones. However, vibration is difficult to measure easily. There have been many reports of utilization of microelectromechanical systems (MEMS) based technology such as this one from Analog Devices that measures the vibration or strain through mechanically vibrating a component that is then measured accurately.


A group of researchers in Seoul have come up with a new way to measure vibration and strength using the same technology that is embedded in a spider's feet. Vibration is important for a spider not only to detect when a prey has been caught but also to recognize and get the attention of its mate. The spiders feet consists of minute cracks that are embedded with neurons. Any vibration changes the gap in the cracks and thus stimulates the neurons.


The researchers published a paper in Nature that described how they had fractured a platinum layer on top of a flexible substrate to produce a sensor. The cracks on the surface of platinum act as a variable resistor and if the cracks changed in the gap then the resistance of the sensor changed. A simple concept but far reaching in its ability to sense even minute vibrations. They further created a more sensitive sensor by forming an array of these sensors. This sensor thus is flexible so can be put on the skin or on any surface and since sound is also minute vibrations, it can function as a very sensitive microphones.


The next step in the development of the sensor would be to create finished products that can be deployed by device makers.

Sunday, 08 January 2017 18:42

Pricing strategies – what makes sense?

How do you price an information or digital product? Lets imagine you think there is a business opportunity in cataloging all the pizza places in the neighborhood. This short blog is not about whether such a database is profitable or a viable business in the age of easy google information but rather how do you price such a product.


The interesting fact about any information product is that it costs significant money to create the product. Yeah, that is true of most products! But then, making a copy of the new product is relatively cheap. Or providing access to the product is relatively cheap. So lets say it costs you $10,000 to create such a database. Now, you have a customer who says they would like to have access to the product. What would a company sell the access to the database for ? It costs nothing to the company to provide access except some server or storage costs which are essentially negligible.


Would your company allow access for $1? Cheap!

Would it allow access for $10,000? Expensive!


So how do you come with the right pricing? The company cannot base the selling price based on the price that it costs to make a copy. $0.01. In an older economy, the way to price it was to say that it costs me $x to make the product and I will sell it for $x + 30% margin. All very well.

One complication would be that your customer can probably get the list for free from Google. In which case whatever you charge is a premium. Which means that your company needs to provide the data in some nice way, qualified, or with some value add that Google does not provide.


However, assume that in this case your company does not have any free competition but paid one. That makes it easy – you can price your company very competitively and hope to snatch some business.


One way that economist suggest is that the price should be based on what the market can bear rather than the inherent value…. Which means that charge as much as possible which the customer will pay… This does not sound right… but what do you think?

Saturday, 07 January 2017 16:05

Competition is expensive




The capitalistic economy believes that competition is good and useful to keep prices “competitive” and good for coming up with new technologies and products. In the macro-economic area, that makes perfect sense.


However, from the company perspective, competition wastes resources. If your company is competing on price, rack space and just thinking more about innovation than thinking about innovation, then its wasting resources.


Consider the picture above in a grocery shelf for “Soy sauce” If a company makes soy sauce and assume it is coming up with what it considers a novel product. Soy sauce made from shrimp instead of fish. Do the purchasers care? How does it distinguish itself in the grocery shelf isle. The company will probably spend extra in paying extra in getting its product placed favorably in the center shelf or probably more in the end tab zone. It will then start spending money on advertising, offering sales, and in general getting them in specialty stores. They would then employ more sales people that would go and flaunt the product all over.


The competition factor makes it uneconomical for any company to come up with a new product that it will not be able to sell efficiently. The one way that the would be able to sell would be if they had a new product that no one else made and that they could market it efficiently to their customers.


How would you market the soy sauce for a company?

However, note that it IS regulated by the Regulation CF and there are several guidelines that govern. For example, there is limitation on investment in a 12 month period per individual – so you can invest about $2k to $100k (for high net worth individuals). Note this is not something that you do casually – this needs to be mediated through brokers or funding portals.


Other rules: You can only raise $1MM per calendar year through the crowdfunding portals. It does not restrict you from raising money through other channels.


The company raising money has to keep almost everything disclosed – any material information, description of financial stats, two years of financial statements and there are some tiered reporting guidelines from simple; tax statements to more complex like CPA review to a full audit.


Check out some crowdfunding portals as in investor or for your company which are regulated by the financial regulators:



As investor, remember – these are early companies and most will NOT make you money.

As a startup – you have obligation to your investors and follow the rules.

Monday, 08 September 2014 11:33

The curious case of data mining Octopus

Did you know about Paul the Octopus who could predict soccer matches? Since 2008, Paul the psychic octopus has been correctly picking the right team that will win the world cup soccer matches especially Germany in a German zoo. It works like this: to make Paul predict the right match, the zoo keepers in Germany present him with two transparent boxes, each of them labeled with the flag of the competing countries and loaded with a tasty mussel to eat. Depending on which one Paul selects first to eat, is the country that wins the soccer game.

Does Paul know about soccer ? No.

Can he unscrew bottle lids? Yes, the octupus is one of the most intelligent species in the invertebrate world.

Does he predict correctly? Yes, most of the time.

Paul predicted 8 out of 8 games in the FIFA world cup of 2010, which converts to 1 chance in 256.

Probabilities are a concept that we learn during school with a coin toss. If you toss an unbiased coin, then it has an equal probability of falling on either side with heads or tails. Thus predicting 8 straight matches equals 0.5 x 0.5 x 0.5 x 0.5 x 0.5 x 0.5 x 0.5 x 0.5 = 1 chance in 256.

Just from the sheer odd nature of the prediction, there have been numerous articles written about Paul which are convinced that based on sheer statistics Paul was a psychic. A good web search will bring up several articles about his incredible ability. And the more one data mine's Paul's correlations with World cup results, the convincing it gets that Paul had some innate ability (the correlation coefficient is incredible!).After all how could this be possible any other way? So what gives?

It turns out that Paul was in a German Zoo and mostly presented with the German flag to predict the outcome of German matches. It also turns out that octopus like horizontal lines and picked up the German flag for its horizontal lines. Though the octopus cannot see color, if you look at the German flag shown below you realize the image processing in the Octopus eye. Each time it picked up the German flag, it got the tasty treat. Pretty soon, it learned to pick up the German flag first.

German Flag

Somehow, the Octopus gets attracted to the lines, where it also finds food and selects the flag. Curiously, the other times that it has selected the flag, it selected Spain which has similar pattern to the German flag.

Spainish Flag

 And other times, it was the Serbian flag which was also very similar.

Serbian Flag

Thus though the data showed that there was a strong correlation between Octopus picking the right winner and the winner of the soccer game, the conclusion to ascribe it to image processing in the Octopus eye was only possible once the processing in the Octopus eye was understood. Thus, finding correlative data should be a starting point for more investigation rather than a conclusion.


Tuesday, 05 August 2014 15:57

Warheads and Confidentiality


Key by usinlife on Sketchfab

This article is more to do with confidentiality than warheads. There is a proof in cryptography called zero knowledge proof which states that it is possible to confirm a statement from one party by another party without doing a measurement.

A recent paper in Nature has created a zero knowledge protocol to verify warheads without the other party getting any additional information. The example they cite in the paper is with marbles but the method has been illustrated several times. In the marble case in the paper, assume there are 2 boxes of marbles(A1, A2) accompanied by another 2 box of marbles (B1, B2). By giving a verifier-person the ability to randomly combine B1,B2 with A1,A2 to yield equal results increases the chances that A and B are indeed what they are supposed to be…see the paper to get the full description.

These confidentiality measures can probably be used in other areas in healthcare too. In healthcare, it is important to hide the person or information associated with the person so that they person cannot be identified with their medical data. By using the zero knowledge protocol we can verify the confidential information without revealing the information for verification.

Monday, 04 August 2014 15:31

Device Design competitions:

Picture from Blog

Device companies often try to fulfill a need in the market. For example if the need in the market is irregular heartbeat then the companies are tempted to create pacemakers in collaboration with doctors which enable them to create devices that would regulate that heartbeat electronically. However, last year MDDI online came up with a Dare to Dream contest at the link below. Here the practicality or financial numbers were not considered but rather the requirement was to come up with a device that would serve a purpose.

There were several entries that were judged to be really useful.

Third place: This was a device that was a Cerebrospinal fluid pressure regulator. This was created by Bob Paddock who had a very simple design as shown in the picture above. It did not have to be very practical but it had to have the components that were plausible. In Bob’s case there was a personal story since his wife had committed suicide from the pain of leaky Cerebrospinal fluid. This would almost be possible depending on whether there is big enough market for such devices that would correctly diagnose a bad continuous headache.

Second place: Myosense, a tape to collect data on the muscle movement and record that data to enable movement disorders. Again hopefully, there is a big enough market for this but this could have potential utility for a small group of people.

First place: This was an smart phone app that measures the heart activity around the clock. There have been several startups that have targeted this area, from wrist monitors to those that measure the heart with an attachment on the chest, near the heart. It would be interesting to see which of those devices are used every day.

Competitions like this encourage a lot of thought and target need. These are great to determine the market need, though they need to be balanced with seeing the cost impact. For example, you could wear a heart monitor if you are likely to have heart attacks or are in the category that has a potential to develop one, but it will be interesting to see how many people benefit from such devices. It is also worth asking that if you are such a patient, will you trust your cell phone, or would you be more comfortable using a device that has been FDA approved for your security. However, FDA is deregulating several devices as this article discusses in greater detail.

A very concise description of automated blood pressure measurement.

When new medical doctors are taught to take blood pressure, they are taught to listen to the sounds through their stethoscope while inflating and then slowly deflating the arm cuff. This instrument is called the sphygmomanometer. There are distinct sounds that one hears as the artery is occluded by the cuff and then slowly opens when the cuff pressure is increased. Listen to the video below to listen to the sound. These sounds are in 5 phases and are called Korotkoff sounds. They represent blood pulsing past the occluded artery as the artery is opened. This method of blood pressure measurement was colled

Automatic instrumentation to measure blood pressure was being developed and in the earlier generation of machines, they used an audio microphone to measure the sounds. This sometimes led to issues since if the microphone was not in the correct place then the sound could be missed and leading to failed measurements.

New instrumentation was then invented that could still measure the occlusion of the artery. But this time it used a very sensitive pressure detector that detected the oscillation of the artery, rather than the sound, to determine when the artery was blocked and then released. It turns out that from the time of occluding the artery to its opening the artery vibrates. This vibration decreases and then increases and can be measured accurately. This is the principle that is used in most automatic blood pressure measurement machines.



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