Building a Sequencing Data Analysis Platform: A Roadmap and Strategy for Success

Introduction:

With the rise of next-generation sequencing technologies, there is an increasing demand for efficient and user-friendly data analysis platforms. Researchers and organizations require powerful and flexible tools to analyze their sequencing data, extract insights, and make informed decisions. In this article, we will discuss a product roadmap and strategy for building a sequencing data analysis platform that can meet these needs.

Product Roadmap:

Phase 1: Initial Development

The first phase of building a sequencing data analysis platform is to develop the core functionality. This includes building a user-friendly interface, implementing basic data import and processing functionality, developing a pipeline for basic quality control and filtering of raw data, and integrating popular bioinformatics tools for read mapping and variant calling.

The user interface should be designed to be intuitive and easy to use, allowing users to navigate through the platform effortlessly. The platform should have basic data processing capabilities, such as handling raw data files and converting them into usable formats. Quality control and filtering of raw data should be implemented to ensure that the data is of sufficient quality for downstream analysis. Finally, the integration of popular bioinformatics toolsfor read mapping and variant calling is necessary to provide a comprehensive analysis of the sequencing data.

Phase 2: Feature Expansion

The second phase of building a sequencing data analysis platform involves expanding the platform's functionality. This includes adding data visualization and exploration options, implementing more advanced quality control and filtering options, developing additional pipelines for specific analysis types (e.g. RNA-seq, ChIP-seq), and integrating machine learning algorithms for predictive analysis.

Data visualization and exploration are essential for understanding complex data, making it easy for users to extract meaningful insights from their sequencing data. Advanced quality control and filtering options should be implemented to enable users to customize their data processing pipeline based on their research needs. The development of additional pipelines for specific analysis types, such as RNA-seq and ChIP-seq, will expand the platform's applicability to a broader range of research fields. Finally, the integration of machine learning algorithms can provide predictive analysis capabilities, enabling users to make more informed decisions based on their data.

Phase 3: Scaling and Integration

The third and final phase of building a sequencing data analysis platform involves scaling and integration. This includes optimizing the platform for scalability and cloud deployment, developing APIs for integration with other bioinformatics tools and workflows, offering customization options for advanced users, and providing support and training for users.

Optimizing the platform for scalability and cloud deployment is essential to ensure that the platform can handle large datasets and can be easily accessed from anywhere in the world. The development of APIs will enable the platform to integrate with other bioinformatics tools and workflows, providing a seamless experience for users. Offering customization options for advanced users, such as the ability to develop and integrate their own analysis pipelines, will enable them to tailor the platform to their specific needs. Finally, providing support and training for users is crucial to ensure that they can fully utilize the platform and achieve their research goals.

Strategy:

The strategy for building a successful sequencing data analysis platform involves identifying target users and their needs, building a user-friendly interface, implementing robust data processing, developing advanced analysis features, scaling and integrating the platform, and providing support and training for users.

Identifying target users and their needs is the first step in developing a successful sequencing data analysis platform. Understanding the types of researchers and organizations that would benefit from the platform and gathering feedback on their needs and pain points is crucial to ensure that the platform meets their requirements.

Building a user-friendly interface is essential to ensure that the platform is accessible and usable for all users. The platform should be designed with the user in mind, with intuitive navigation, clear labeling, and helpful tooltips. Implementing robust data processing capabilities, developing advanced analysis features, scaling and integrating the platform, and providing support and training for users are also key components of a successful sequencing data analysis platform. By following this roadmap and strategy, you can build a sequencing data analysis platform that meets the needs of researchers and organizations, enables them to extract valuable insights from their data, and accelerates scientific discovery.

  

mRNA vaccine vs other vaccines – Some FAQs

It is late September of 2020 and the Covid19 Wuhan Coronavirus has claimed nearly a million lives in a matter of months. US alone has ended with more than 200 thousand deaths so far, and there are little signs of the death toll abating in the near future. 

The race for vaccine was started right at earnest and progressed through different phases at an unprecedented pace, most possibly over pacing the countless rigors in the process. Given the scale of the pandemic, much of this is to be expected. Among the candidates to make the final cut are the mRNA vaccines, a new type of engineered vaccine hitherto untested extensively in humans. As a result, a lot of questions have come up regarding its safety and efficacy. Here are some of them …

1. What are some benefits and risks of an mRNA vaccine?

The benefits of an RNA vaccine (or mRNA vaccine, as it may be referred to as) stems mainly from the fact that the antigen coding transcripts are directly used by the host cellular machinery to be translated into active components, against which the antibodies shall be raised (by the body’s immune system) (1).

Figure 1: Two categories of mRNA constructs are being actively evaluated. Source: “The promise of mRNA vaccines: a biotech and industrial perspective” – npj Vaccines - https://www.nature.com/articles/s41541-020-0159-8/figures/1

Using this approach has a key advantage. The genetic material in the vaccine doesn’t have to enter the cell’s nucleus and incorporate it into the genome. Instead, it directly uses the translating machinery that converts the transcript into a protein. It is also possible to fine-tune the mRNA transcript by doing some chemical modifications to avoid degradation. 

To use an analogy, you use the ‘printer’ of the cell to print out pamphlets about the bad guy, rather than sending the ‘entire file’ to the cell’s ‘computer’.

The risks are yet to be known in humans since this approach fairly new in clinical practice. It is possible for the mRNA vaccine to induce some unintended immune responses including mRNA-Cargo interactions during the formulation process (2). There is no animal model as yet that matches perfectly with the human responses. 

Another possible concern could be that some m-RNA based vaccine platforms induce some potent type-I interferon responses. These have been known to be associated with inflammation and autoimmune responses. Therefore identifying individuals at increased risk for this would be key to administering this type of vaccine (3).

2. What about any side effects that are concerning? How common are these in such vaccine trials?

In the latest development, researchers at the Massachusetts General Hospital have identified some markers that may predict coagulation assisted complications in patients with COVID-19 (4). The risks for an mRNA based vaccine come with its own flavors besides other usual ones typically associated with vaccine trials. How significantly would they pan out as compared to other types of vaccine systems, remains yet to be seen.

According to the Moderna company’s website (5), their mRNA-1273 vaccine is against the stabilized form of Spike protein (S). Though this portion has remained fairly stable small variants have observed (6). Also, the vaccine is under the assumption that the molecular pathogenesis is from this protein alone. The virus is fast evolving. 

Also, the progression through different phases has been greatly accelerated so far, given the nature of the pandemic. As a result, many approval steps may have had to be rushed through, for expediency; one may have to assume that all these steps must have been duly vetted out as well.

3. What makes up for a very promising vaccine trial and convince someone to sign up for this trial vs. other vaccine trials?

The website of the company should have a clear and transparent timeline of the progress of the vaccine development so far; starting from their initial procurement of the sequence data and the contract date till today. It would be therefore possible to get an idea of the way in which the results are going to pan out, assuming the site continues to keep it that way (7). 

4. What is the ideal sample size for a Phase 3 study of such a vaccine trial? Can numbers alone suffice?

A couple of recent ongoing trials (8,9) have decided to enroll about 30,000 for their Phase 3 of clinical trials, and this is a fairly good enough for a phase trial of this size. Most of such trials run into few thousand anyway. The greater question should be if there is time enough for follow up studies to study the efficacy and safety (10) and observe for any adverse events. Given the current nature of the pandemic that again may have to be ‘accelerated’. How that may pan out to assuage the concerns of the public before public release is a different matter.

5. What does this Phase 3 study need to prove that it is a good vaccine?

Firstly, the vaccine has to be shown to be widely effective, matching up with beyond the success rates of the other vaccine trials. In addition to this, adverse events must be very insignificant in comparison to the rates for other vaccine therapies. All of these results must be publicly available and transparent, of course.

6. What is ‘vaccine efficacy’ and how would a ‘50% effective’ vaccine match up to one that is 70% effective? Can we expect one that is 70% or more effective?

An informal search on the web shows any trial success above 50% is good enough, 60% would really pushing it. I am not aware of 70% success rates, great if it does. A recent study by researchers from MIT looked into the success rates of Vaccine trials vs therapeutic trials and found that they were more likely to hit the dust than their non-vaccine counterparts BUT that reason has been mainly attributed to lack of investment and efforts, in the recent decades, in finding the ideal approaches to delivering vaccines effectively (11,12).

Numbers aside, at this point the aim should be mainly to increase the absolute numbers who are successfully immunized and can thus add up to the herd immunity. 

Also, this being an mRNA vaccine, the first of its kind in a worldwide major trial, is likely to be recorded in itself. Given the theory behind the vaccine, the success rate can be expected to be pretty high like its other counterparts.

7. What about some common fears, misconceptions, or misplaced logic?

Despite the year being 2020, the fears and myths against vaccines have grown so exponentially in the last few years that one would wonder … Well! There are any number of myths and all of them debunked as well. 

One of such misplaced logic, of particular relevance to the current pandemic, is "allowing herd immunity to do its job"! This is another way to skip vaccines under some pretext at a great cost to public health. To put it simply, it sounds like a game of Life-roulette.  Consider this! We have witnessed 200 thousand deaths in a matter of months and still counting!!! The US has probably never seen anything like this. As if gambling with one’s life were not enough you are just endangering everyone out there.  There are countless instances of people resorting to such an approach and regretting it badly. Not worth it! On the other hand, there are nations that have successfully taken active measures in this regard. One should learn from them and allow Science to do its job.

8. Why is it important to volunteer? How to allay fears of the risks?

The success of a clinical trial exclusively depends on the active participation of healthy volunteers. Consider this! If you can get a thrill out a rollercoaster OR bungee jump then this is far better; you become a hero helping science advance further for public health. In an open and transparent setting of a clinical trial, the volunteer will and should have access to all that entails the participation.

 

Understanding personality assessment in a dynamic situation involving personality interactions

I just chanced upon one of those 'personality tests' based on the famed Myers-Briggs Personality test and yeah! had some fun with it playing with different answers. Different sites provide different versions. I happened to choose 16personalities.com. You can choose the one you want but regardless of the one you take you arrive at a result that comprises of four alphabets. Now this combination is what holds key to your 'supposed' personality. These scores are used from personal amusement to even serious  evaluations. 


Then I wondered something - the very nature of this test is single person oriented i.e. mostly self assessment report and sometimes (possibly) from another person's viewpoint. Most importantly, this is not a test but more of a personality type and preference. While ducking and dodging the semantics for any judgmental tones, it is safe to state that what one assesses about themselves is certainly not going to be what the other person were to do about them (and rightfully so). 

Since we tend to live in an interactive and social environment all these personality type scores have little meaning without an interactive score pattern and then start understanding the variations. This, I feel could lead to better assessments, even if for fun. So tomorrow if someone were to develop an interactive app that combined them into the type of matrix (let's call it #PAMatrix), don't be surprised 😎 I told ya!

Image Source: Wikipedia

The Personality Assessment Matrix – PAMatrix

There are different types of personality assessment tests like the Myers-Briggs Personality test. Regardless of the type of test administered, there is always a score. It could be a number OR a combination of alphabets OR even very 'subjective' as some would like to prefer it. Now! Such an evaluation can be done in different ways

• Self-assessment
• Assessment by others
• Assessment by ‘qualified experts’
• Assessment by those known to the person

The scores are likely (more so) to differ in each of the cases and quite possibly, rightfully so. So! Which one of the scores is right OR are all of them right in their own way? If the latter is true, then therein lies the undercurrents of perception, image building etc.

So, to better understand this, the whole assessment of a personality in an individual can be expressed in the form of a MATRIX. Since it is a matrix centered on the personality of an individual, let’s call it the PAMatrix. This kind of a matrix is rooted in the principles of interaction of a person with others around him/her in the home, workplace or public in general. Since this is what basically constitutes our society, any personality assessment has to be seen a whole of different perceptions when it comes to evaluating a personality.

	X	Y (X)
X	What X thinks of 'Self'	What X thinks Y will estimate about 'Self'
Y (X)	What Y thinks of X	What Y thinks X will estimate about 'Self'

Table1- The Personality Matrix or the PAMatrix

It is the analysis of this matrix that is going to define the concurrency of the evaluation process and reconciling the differences that ensue.

Case analysis

	X	Y (X)
X	ENFJ (Protagonist – Diplomat)	ENFJ
Y (X)	ESTP (Explorer – Entrepreneur)	ESFJ (Sentinel – Consul)

Table 2 Case study 1

Let us consider the following case of a person X. Applying the matrix above let us consider a possible scenario below using the Myers-Briggs Personality test. The descriptors for each result have been conveniently taken from 16personalities.com but one could refer to any site that gives them suitable names. 

In the above case

1. X rates himself or herself the same as s/he would think others would rate him/her. Now this is good in a way. Some coherence there though the scores could certainly change when others see it. 
1. If the score of X↔Y(X)were different from X↔X, then any discrepancy here could mean uncertainty in the image being projected. This could be something to work on.
2. Y evaluates X differently. Now! This is a regular scenario since we are not perceived the same as we think we like to be perceived as. Everyone has their own benchmark and priorities and hence evaluations will certainly vary here. If there is indeed any consistency here with the scores that X has valued themselves at then it is indeed an achievement to the efforts by X to project that image.
   
    The bottomline is that, the more closer this score tends to X↔X and X↔Y(X) the better the consistency in the image portrayed and hence it more likely to lead to better relations between X and Y. On the contrary, if they are strikingly different then efforts have to be taken to address such a difference. Hence this is something to work on again.
3. The final and probably overlooked one is the Y(X)↔Y(X) match. A typical scenario would be when worker says, “The boss thinks he knows it all when actually he just manages them well without going into details”. This is a telling statement and gives room for greater understanding. Some of the differences maybe natural by virtue of the interaction involved e.g. a boss interacting with many people reporting to him. However, some others could be important especially in a 1-1 interaction scenario where differences exist between the individuals.

So what do you say? Ready to try this out with someone else and see how the matrix turns out? 👍

Will the Bayer-Monsanto deal submerge the anti-GMO mindset?

Yes, the word is out and deal is inked. Bayer has clinched a $66 Billion takeover deal of Monsanto. Two big names, becoming one big(ger) name. The tectonic plates in the AgroBiotech industry are rattling big time - Dow and Dupont merger involving $130 billion, ChemChina acquiring Syngenta for $43 billion. Completion of these merger would leave these three companies with more than 75 percent of the global market i.e. US, Germany and China.

Image source: Wikipedia - Traditional farming with oxen in India.

Notwithstanding the impending political and consumer scrutiny, these moves are certainly and steadily going a long way in addressing and controlling world food markets. While China will have the powerhouse of Syngenta's plant-genomics R&D (and hence less outside control), India would be laying itself open to the grace of Bayer (instead of Bayer and Monsanto).

So what does this have to do with 'submerging the GMO mindset'? I am not a finance or a market geek, but more of a science (and it's effects) point of view, person. To us all, till now, blaming GMO meant blaming ... well... Monsanto. You always thought that evils of GMO meant Monsanto right! The name became synonymous with all things bad in plant science besides their monopolistic business practices (not that they were, or, are alone out there). Re-branding wouldn't have helped either 'cos it would be the same issue of GMO once again. On the other hand Bayer, as a brand name , encompasses a wider variety businesses than just GMOs. It also has it's own brand identity. So, looking at it from that angle, there may not have seen a better way out than this. Same goes for, probably, Syngenta-ChinaChem.

Meanwhile this deal also apparently throws doubts over the GMO revolution and the dominance of genetically modified crops - quite counter-intuitive sounding. According to this article farmers are apparently reconsidering the use of biotech seeds as it becomes harder to justify their prices amid the measly returns of the current farm economy. Hence a question arises if such a deal like Bayer-Monsanto or ChinaChem-Syngenta is also an attempt to effectively address the rising costs of Biotech R&D. What I see gradually happening is a shift in this anti-GMO mindset by internalizing such GMO entities it under bigger brand names doing other things like crop protection and agrochemicals. This buy-over will certainly give Bayer the next tag of the 'GMO bad boy' BUT only for a short while. Public memory is short lived you see. So, for now, all of you #BlameMonsanto guys have to rethink your next favorite whipping boy.

Leukemia Survival Curve - Estimates

I have presented below a simple interactive spreadsheet giving a brief outlook of the life expectancy upon diagnosis of the type of leukemias listed below. The list will keep changing as more types will be added. This feature best accessed from desktops and may not work well in mobile phones or devices.



NOTE: The information presented below are projected values based on SEER Survival Data from the SEER Database - http://seer.cancer.gov/ . Values and results provided are for information purposes only. Actual results may vary based on health of individual like ECOG score, success of the proposed treatment in clinical trials, besides other  factors. No responsibility is claimed whatsoever.  

natarajanganesan gmail

‘What should define a well meaning opposition’

Bedlam in a Parliament

What is it with the discussions in the parliament across the world? I just saw a video of bedlam and chaos in a country’s parliament. Next I see few more more trailers posted below from other countries and the scene is no better or worse. The comments below the video are even more revealing. Nearly every user from every region and place has the SAME old thing to say - how even their place is no better, just the dresses and places are different. Instead of going into the usual blame game and ‘how all politicians should be bundled up and thrown out’ I want to ask something different - something more 'theoretical' and that requires deeper introspection.

The question is simple, 'What should define a well meaning opposition'?

In other words what are the policies where parties could differ, and what are those issues on which there should be no argument or chest thumping i.e. they are a given.

Before reaching out for answers, I want you all to consider a couple of things. There is an inherent paradox (or dichotomy, if you will) in asking such a question YET so relevant and crucial in defining of a functioning house. This is under the assumption that all members are conscientious on both sides of the table (hence the word 'theoretical' :) ).

I am bringing this issue because, today I find many a party (be it anywhere) at cross-roads with the system that sustains it. Someone chest beats about patriotism as if it were their birthright while someone assumes they are indeed the people to think of equality of existence for all. Things are so bad that yet another party claims it right to being 'clean' and working for the people. All these things should NOT be defining the basis of a party formation but should be common across the board.

I could rattle on BUT what do you think?

Tag-cloud your professional summary, not your resume!

They say ‘a picture is worth a thousand words’. I’d go a step further and say that ‘a picture of words (effectively designed) is worth a thousand times more’. That brings me to the topic of using tag-clouds as a supplement/complement to your professional summary.

Wikipedia defines as a tag cloud as follows - A tag cloud (word cloud, or weighted list in visual design) is a visual representation of text data, typically used to depict keyword metadata (tags) on websites, or to visualize free form text. Below is an example of what I talking about.

For those who are already aware of this concept, it must have struck you at some point of time as to why it has not made its way into resumes. For now it looks a bit jazzy to see them in your CVs or resumes but it’s worth noting their advantages when you are looking at compressing content effectively where space is a premium.

Advantages
When used and placed appropriately in resumes, tag-clouds can greatly enhance the content. What is referred to as keywords (a table) in resume can be effectively replaced by tag-clouds. Resume-builders could effectively build some acceptable templates

Disadvantages
The keyword here is effective crafting of the summary. You don’t want the picture to reflect that are mostly job requirements as opposed to crucial skill-sets you bring to the table. There are a couple of videos out on the internet that give you examples of this.

What you can do …
If you use one of those online tag cloud generators here are a couple of things you can do

1. Give weightage to your own words – That is, if you can really visualize how you see the words. Since these programs often operate based on the number of times the word is used, you can literally create a garbled text of these words repeated as many times as you wish (for each word). I have actually seen it to work :) 
2. Create an effectively designed professional summary – In other words if you have taken pains to create a well-crafted professional summary, you may as well use that and fine tune it a bit. It is here that a well composed summary of your in your #LinkedIn #Profile might actually be of help. Just copy that into your program and watch the results. Play around a bit with the fonts and presentation. You might actually like it!

A final note

There are many online free tag cloud generators. Wordle is by far the popular one but they are getting fancier (fonts, color, presentation etc.).  Tagul allows you play around with shapes (even your own photo upload). I guess it will only be a matter of time before it will become a norm to see it in resumes.

In fact, one of the best places where it can be used effectively is the back of business cards. Imagine every professional business card having this in fancy ways. Or imagine in a Harry Potter style, you can just click on the email in the card and send a video message. Quite fancy eh! My coffee just got spiked again :)