Notas

● Is “bioinformatics” dead?
The field is still alive, but it´s name no longer applies to what´s done in it.
Author´s POV: until the 80s/90s, computation was a complex tool, but the human
genome project change this - experiments and computation were synergistic, and of
course, the promise of bioinformatics came to help (by describing and maintaining
loads of digital data that was being generated and to provide the tools needed to
assemble 3 billion nucleotides).
Yet some years after the 00´s, bioinformatics could not deliver what was expected by
the industry. In the meantime, a new generation came in, making bioinformatics
spread its wings as a computational biology and then systems biology. But what lead
to this changes: digital data.
What´s data science? Long story short, it´s part computer science, part statistics,
part information science, and part applied math.
The 4+1 model: the "4" refers to systems, design, analysis, and value, and as for the
"1", to all the disciplines/domains witch we can apply the "4".
Each of the "4" helps influencing the "1".
But how do they influence?
Systems: high performance computing, cloud environments, high-throughput

systems, workflow systems, benchmarking analyses, cyber security (all adjusted to
the needs of big data);
Design: the relationship between data, computers and humans at all stages of the
data life cycle (from ingestion to visualization, and other forms of dissemination;
Analysis: comprises techniques seeking both causality and prediction such as deep
learning, data mining, and natural language processing:
Value: tension between the value that an analysis brings vs. The unintended
negative consequences that can result and how to strike the right balance.
Author´s conclusion: we need to become biomedical data scientists.

● Bioinformatics: Basics, Development, and Future
Biological data can be described as molecular sequence information and

“wet-bench” experiments. Bioinformatics targets to develop methodology and
analysis tools to help with biological data (store, organize, systematize, annotate,
visualize, query, mine, understand, and interpret complex data volumes). It uses
conventional, modern computer science and cloud computing, statistics, and
mathematics, as well as pattern recognition, reconstruction, machine learning,
simulation and iterative approaches, and molecular/folding algorithms. The advances
of this field, are mainly associated to the computerized programming and software
developments needed for the handling and structural and functional analysis of large
volumes of molecular sequences.
Bioinformatics shouldn’t be mixed with biometry and biostatistics, development of

DNA computers, or computerized generation and filing of data from imaging. Besides
it should be differentiated from related scientific fields such as biological computation
and computational biology.
Bioinformatics develops and utilizes computational algorithms to understand and

interpret biological processes based on genome-derived molecular sequences and
their interactions. It focus on providing practical tools to organize and analyze basic
genomic, proteomic, etc data, including sequence analysis and its visualization. The
common core aims of the field, are to handle, analyze, and interpret the
genome-derived molecular sequence data and its organizational principles in broad
scales/spectra of comparative, simulative, and evolutionary/phylogenetics
perspectives. These tools can be applied to other fields like biochemistry, agricultural,
medical and environmental sciences, and artificial intelligence too.
Bioinformatics tools help to interpret and understand the molecular and evolutionary
processes and interactions from large volumes of raw data in the field of wet-bench
experimental molecular biology. All of these large scale, genome-derived, molecular
sequence analyses of raw “Big Data” are impossible to be analyzed manually, in
result scientists had to come with interdisciplinary methods that resulted in the
bioinformatics science.
History of emergence and development
Bioinformatics term was coined by Paulien Hogeweg and Ben Hesper in 1970, and
referred to the study of information processes in biotic systems like biochem and
biophysics. However the emergence to it tracks back to 1960s with Frederick Sanger
and his discovery of the sequence of insulin in the 50s.
Bioinformatics help in handling and analysis of the
genomics data, genome annotation, and expression profiling
Rapid and reliable determination of DNA molecules, was a need because of the
introduction of the sequencing technique of Sanger and Coulson and Maxam and
Gilbert(large scale DNA sequence data that needed to be analysed by computerized
programming).
Thus, without bioinformatics tools, it’s impossible to think of genome sequencing,

since these tools help not only to handle, analyse, compare, relate, and visualize
DNA sequences, but they do also offer help with the sequencing process itself. The
creation of cost-effective, next generation sequencing (NGS - massive parallel
sequencing technology) platforms has helped to completely decode nearly the entire
genome of many different organisms.
Bioinformatics tools are needed in annotation and prediction of genes from

sequenced genomes that requires computerized approaches because genomes are
large to be manually annotated. Also these tools are very important to analyse gene
and protein expression profiles.
Bioinformatics plays a major in data collection of the functional elements of

sequenced genomes that use the next-generation DNA-sequencing technologies and
genomic tiling arrays.
Structural bioinformatics: molecular folding, modeling,
and design
Some of the most used applications of bioinformatics is identification of

three-dimensional protein structures, molecular modeling, and folding to predict the
possible function of proteins or other molecular structures, model behavior of
molecules, fold the molecule to its native biologically functional three-dimensional
structure, and design biomedical drugs for many complex human diseases.
Biological networks and system biology
In 1998, Watts and Strogatz, and then in 1999, Barabási and Albert fueled the
opinion that complex systems can be viewed as networks where components can be
represented as nodes and they are linked through their interactions. The properties
of nodes and edges form the network topology.
Bioinformatics approaches are also the core for building, organizing, and
systematizing biological networks of molecules, and genetic and biochemical
pathways of complex cellular processes.
Databases
An organized collection of data is referred to as database that aims to collect

schemes, tables, queries, reports, images, and other objects. And the access to the
databases is provided by an integrated set of computer software, called “database
management system” (DBMS). The DBMS allows the user to access all of the data
contained in the databases, as well as having general functions for data definition,
entry, storage, update, administration, and retrieval of large quantities of information
in an organized way that requires modeling, clustering, query languages and query
optimization, and visualization algorithms.
Development of databases, is significantly dependent on bioinformatics tools,

advances, research, and applications. There’s a large number of different types of
databases available, that cover all aspects of biological data storage and
organization.
Software, analysis tools, services, and workflow
Software and analysis tools, and bioinformatics services and workflow have been
the main fields and core targets of bioinformatics since its emergence. Since the
development of the first bioinformatics software and analysis tools in the early 1980s,
many free and open-source software tools have been developed and continue to
grow and improve with the advancement made in genomics sciences.
Development of sharing models and web access tools is also an important objective
that allows users to utilize and access tools over the internet and from their computer
systems.
Some web service-based bioinformatics analysis resources represent a collection of

standalone or web-based interface data analysis tools as well as integrative,
distributed, and extensible bioinformatics workflow management systems (BWMS).
The BWMSs are designed specifically to compose and execute a series of interactive
computational or data manipulation steps in analyses.

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● Is “bioinformatics” dead?

Each of the "4" helps influencing the "1".

But how do they influence?

Systems: high performance computing, cloud environments, high-throughput

Author´s conclusion: we need to become biomedical data scientists.

Biological data can be described as molecular sequence information and

Bioinformatics shouldn’t be mixed with biometry and biostatistics, development of

Bioinformatics develops and utilizes computational algorithms to understand and

History of emergence and development

Bioinformatics help in handling and analysis of the

genomics data, genome annotation, and expression profiling

Thus, without bioinformatics tools, it’s impossible to think of genome sequencing,

Bioinformatics tools are needed in annotation and prediction of genes from

Bioinformatics plays a major in data collection of the functional elements of

Structural bioinformatics: molecular folding, modeling,

Some of the most used applications of bioinformatics is identification of

Biological networks and system biology

An organized collection of data is referred to as database that aims to collect

Development of databases, is significantly dependent on bioinformatics tools,

Software, analysis tools, services, and workflow

Some web service-based bioinformatics analysis resources represent a collection of

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