computational biology?
On this
ACADEMIA | Letters
Innovating with
Biomathematics: the
challenge of building
user-friendly interfaces
for computational biology
Jorge Guerra Pires1, PhD (Founder at
IdeaCoding Lab)
Independent Researcher/Member of
the Center of Excellence for Research
DEWS (University of L’Aquila,
DISIM, Italy).
jorgeguerrabrazil+academiaedu@gmail.com
Abstract. Web development
became an omnipresent demand
on modern age, also in scientific
computing. How does one can
take advantage of this ever-
growing trend when it comes to
1
https://orcid.org/0000-0002-5786-0306
Academia Letters, June 2022
Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com
Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792
short assay, we shall learn about
how web development can be
used to support medical doctors
on decision making.
Keywords. Computational
intelligence; computational
biology; systems biology;
bioinformatics; startups;
JavaScript; web development.
Introduction
The medical sciences started out their path
as a “holistic” discipline: the information
they used to make use of reality was not
first-hand, and theories were mainly
speculations. In the last centuries, more
intensely in the last decades as a result of
several technological developments, the
medical sciences have been bombarded
with a wave of new technologies and
paradigm shifts coming from almost all
possible directions, especially coming
from computer science and mathematics.
On this short assay, we focus on how
computer and mathematical endeavors
can be used to be innovative on medicine;
I am thinking of startups, the current
innovative “buzz word”. Since this is a
short letter, we just scratch the surface. I
©2022 by the authors – Open Access – Distributed under CC BY 4.0
1
have a course on the topic with more
details on Udemy2, for the interested
readers.
As a result from a postdoctoral
fellowship research period Pires (2021), I
have done the talk Innovating with
Biomathematics: the challenge of
building user-friendly interfaces for
computational biology (Thursday
Morning Science, 2021). This is a short
assay/paper/communication version of
the talk, merged with new insights after
the talk and the research period.
A considerable amount of thought
herein are a distillation of Pires et al
(2021), seen from another perspective,
more distant from the coding part, which
is more technical. Herein, I want to lay
down a theory, if I can call this reflection
so. This theory can be interesting to
computational biologists and web
developers to create innovative systems
that use models as their inner-working
gears; herein, I am using computational
biology and computational intelligence as
generic terms to related areas, e.g.,
computational biology encompasses also
systems biology, and computational
intelligence also encompasses artificial
intelligence. Thus, I kindly invite the
readers to think all these scientific areas as
one, one single piece of endeavor, and the
2
Innovating with Biomathematics: The
challenge of building user-friendly interfaces for
Academia Letters, June 2022 ©2022 by the authors – Open Access – Distributed under CC BY 4.0
Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com
Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792
2
final goal is creating online platforms for
supporting medical doctors and
biologists, life scientists in general, to
solve their daily-professional problems.
The most ubiquitous one is decision
making, e.g., is this patient sick or no?
should I consider this diet or not? would
this species vanish or not? would the
COVID pandemic spread or not? All
those questions are decision making
scenarios, which can be aided by models.
Innovation and publications:
how publications can hinder
innovation
As Spicer and Roulet (2014) bring to
attention “as a direct consequence,
established journals are usually biased
against innovative work.” Additionally, I
heard during my postdoc from an
innovative researcher in healthcare about
the prejudice against people that innovate,
which means less publication in the
traditional sense; mentioning it since I just
published a book on the topic (Pires,
2022), on how Publish or Perish (POP)
has created several issues in science, one
of the them is regarding innovation, taking
knowledge from science to society.
computational biology. https://bit.ly/39coMds
Innovating with biomathematics is all
about how we can use our models from
computational biology (e.g.,
mathematical biology) to support real-
scenarios, instead of just publishing them,
creating a dead end for innovation.
Sometimes, I wonder how less Google™
would have done if they were concerned
about publications. As one example, I do
believe that TensorFlow.js Nielsen et al
(2020), the Google’s version of the classic
TensorFlow Rundo and Tangherloni
(2017), used in deep learning, can be quite
imperative in innovating with
biomathematics. A considerable amount
of works is done in medicine are using
artificial intelligence, see my postdoc
report (Pires, 2018).
Risk of innovation vs. risk of
market: how it can impact
innovating with
biomathematics?
Blank and Dorf (2012) organize startup
endeavors in three groups, when it comes
to risk: i) innovation; ii) customer/market;
iii) both innovation and customer/market.
Innovating will biomathematics will fall
into the 3rd situation. From one side, we
have the risk of innovation since
computational biology in general is based
on ongoing researches, both from the
biotechnological and from the
computational biology side (e.g.,
precision medicine and targeted therapy).
Once one gets the system working
accordingly, one may have the risk on
costumer/market: the usage of
mathematical models in medicine. One
point that I like to defend on this scenario:
do not wait for the model to be perfect,
startup entrepreneurs, they use the market
as compass, called ‘pivoting’, we could do
so as well when innovating with
biomathematics.
The culture of using computational
biology models on real-world scenarios is
an ongoing branch; platforms like the one
proposed by Pires et al (2021) hope to
support it accelerating by offering easy-
to-use platforms, that can be used to
support on weighing the medical
diagnosis decisions (Figure 1).
Figure 1. Going from models to
innovation.
According to online discussions with
two experts on the field, namely
(Kolodkin, 2021; Karr, 2021), some
challenges those models may face, which
can be classified as innovation risk, and
even market risk at some level: i) the
models currently cannot represent the

Academia Letters, June 2022 ©2022 by the authors – Open Access – Distributed under CC BY 4.0

Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com

Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792

3
reality, as so (Karr, 2021) is extending his
famous and respected model for including
human cells; Kolodkin, (2021) discusses a
possible, I would say a distant, future of
virtual humans. Thus, the innovation risk
here is the fact that even though on
academia those models are widely used,
on real world they are quite limited for
explaining complexity. In part, this is
because they depend on medicine and
biology: recently, the Nobel prize was to
David Julius and Ardem Patapoutian “for
their discoveries of receptors for
temperature and touch”3; imagine
someone modeling this system, now they
have to revise their model, for the better.
How much do we have to
know to predict? do not
mistake understanding with
prediction! The illusion of
validity4
Innovating with biomathematics is all
about using models to assist on decision
making.
Are models reliable?
3
https://www.nobelprize.org/prizes/medicine/2021/
press-release/
4
Based on Pires, JG. How much do we have to
Academia Letters, June 2022 ©2022 by the authors – Open Access – Distributed under CC BY 4.0
Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com
Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792
4
We have essentially two big models
when it comes to computational biology:
black-box vs. white-box models. They
are, respectively, top-down vs. bottom-up
approaches. They differ essentially on
what they use mainly as main ingredient:
the former uses data, lots of data; the
latter, theory, “first-principles”.
Example of black-box models are
artificial neural networks, used on
machine learning, e.g., deep learning;
example of white-box are differential
equations. When it comes to human-like
decisions, black-models may be the best.
For instance, they can be easily used to
decide on data-based if a patient is sick;
whereas white-box models are mainly for
understanding a system, simulating their
behavior. We may say that black-box
models are the closest one to be applied in
innovation. Machine learning is
everywhere, see Nielsen et al (2020) for
very interesting applications of deep
learning on several problems outside
medicine; I have some examples on my
postdoctoral report for medicine Pires
(2018).
Sunstein et al (2021) presents some
intriguing insights about models,
including medicine: “In one of the three
know to predict? do not mistake understanding with
prediction! The illusion of validity. Published in
DataDrivenInvestor, 2021. https://bit.ly/3vS0kFR
samples, 77% of the ten thousand
randomly weighted linear models did
better than the human experts. In the other
two samples, 100% of the random models
outperformed the humans.”. For medical
context, the interesting of innovating with
biomathematics, they cite Meehl (2013),
which presents several cases where
models were able to outperform humans:
they call it mechanical vs. clinical
judgments.
How much does it cost?
One of the pillars behind my assertion that
the time is ripe to innovate with
biomathematics is how much we have
now for free. On Pires et al (2021), I have
built in collaboration a full platform for
computational biology, back and frontend
without any cost: the codes are MIT
license. And it is not an exception. Even
though Matlab® and Mathematica® are
paid, and quite powerful, we have
alternatives for free, e.g., Octave and
Scilab. For the frontend, as an example,
mathjs is free, and do a lot, even symbolic
calculation Pires (2021b); even
Mathematica® has a set of free open
access packages for web applications
Pires (2021b).
Nowadays we have what I like to call
“the culture of free for small”: you can use
for free, should you want to scale up, you
Academia Letters, June 2022 ©2022 by the authors – Open Access – Distributed under CC BY 4.0
Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com
Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792
5
pay as you need, on demand. This is
perfect for innovating.
Advantages of web
applications for innovating
“are we still desktop applications driven?
I think not” (Pires, 2021c).
Without being detailed, strong suits of
web applications, compared to desktop: i)
Simplicity; ii) Aesthetic; iii) Updatable;
iv) Efficient; v) Removable; vi)
Supported.
Final remarks
As final remarks, based on my researches,
we have a time ripe for mathematical and
computational models in medicine. I do
believe that innovation may be the best
path, compared to simple academic
studies; the academics either shift to
innovate or some company such as
Google™ may take the lead, as they have
done in several areas such as self-driving
cars. I hope we academics would wake up
and do not let this important task to others,
since most of the hard work we have
already done, the last steps are relatively
simple.
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Academia Letters, June 2022
Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com
Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792
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ntPDLcU&t=6s. University of L’Aquila.
Title: Biomathematics: the challenge of
building user-friendly interfaces for
computational biology.

Academia Letters, June 2022 ©2022 by the authors – Open Access – Distributed under CC BY 4.0

Corresponding Author: Jorge Guerra Pires, jorgeguerrabrazil@gmail.com

Citation: Pires, J.G. (2022). Innovating with Biomathematics: the challenge of building user-friendly interfaces
for computational biology. Academia Letters, Article 5792. https://doi.org/10.20935/AL5792