Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Moore, Benjamin; Carvajal-López, Patricia; Chauke, Paballo Abel; Cristancho, Marco; Angel, Victoria Domínguez Del; Ghouila, Amel; Gopalasingam, Piraveen; Guerfali, Fatma Z.; Matimba, Alice; Morgan, Sarah; Oliveira, Guilherme de; Ras, Verena; Reyes, Alejandro; Rivas, Javier De Las; Mulder, Nicola

doi:10.1371/journal.pcbi.1009218

Cited by 9 publications

(6 citation statements)

References 22 publications

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“… Counsell (2003 ) also discusses the difficulties to teach bioinformatics because of the students lack of previous computation basic skills. This scenario is worsened in low and middle-income countries, with less courses, workshops, and financial support than high-income countries ( Moore et al, 2021 ). In Brazil, it is necessary to mention that digital inclusion is also unequal, even among health professionals ( de Moraes et al, 2009 ), and computational infrastructure is not always ideal ( Rocha et al, 2022 ).…”

Section: The Brazilian Bioinformatic Challengementioning

confidence: 99%

Brazilian women in Bioinformatics: Challenges and opportunities

Kowalski,

Giudicelli,

Pinho

et al. 2023

Genet. Mol. Biol.

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Bioinformatics is a growing research field that received great notoriety in the years of the COVID-19 pandemic. It is a very integrative area, comprising professionals from science, technology, engineering, and mathematics (STEM). In agreement with the other STEM areas, several women have greatly contributed to bioinformatics ascension; however, they had to surpass prejudice and stereotypes to achieve recognition and leadership positions, a path that studies have demonstrated to be more comfortable to their male colleagues. In this review, we discuss the several difficulties that women in STEM, including bioinformatics, surpass during their careers. First, we present a historical context on bioinformatics and the main applications for this area. Then, we discuss gender disparity in STEM and present the challenges that still contribute to women’s inequality in STEM compared to their male colleagues. We also present the opportunities and the transformation that we can start, acting in academia, inside the family and school environments, and as a society, hence contributing to gender equality in STEM. Finally, we discuss specific challenges in the bioinformatics field and how we can act to overcome them, especially in low and middle-income countries, such as Brazil.

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Section: The Brazilian Bioinformatic Challengementioning

confidence: 99%

Brazilian women in Bioinformatics: Challenges and opportunities

Kowalski,

Giudicelli,

Pinho

et al. 2023

Genet. Mol. Biol.

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“…training that is given in languages that some participants may not fully understand 7,8 . For example, genomic and bioinformatics courses are held in English for participants in Egypt, where most people speak Arabic 9,10 .…”

Section: Curriculum Development One Barrier In the Development Of Tra...mentioning

confidence: 99%

Bridging the gap in African biodiversity genomics and bioinformatics

Sharaf,

Ndiribe,

Omotoriogun

et al. 2023

Nat Biotechnol

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“…Python usage has seen a dramatic increase in the previous decade, as the scienti c community has avidly accepted this programing language due to its high applicability, ease of use and modularity (Muller et al, 2015, Harris et al, 2020. Thus, training in bioinformatics and programming has now become a necessity for every life scientist to allow researchers to handle and analyze their data e ciently (Via et al, 2013;Moore et al, 2021). However, in low-income countries and countries with poor science funding it is very di cult to incorporate that kind of training at different stages of scientist research career (Moore et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, training in bioinformatics and programming has now become a necessity for every life scientist to allow researchers to handle and analyze their data e ciently (Via et al, 2013;Moore et al, 2021). However, in low-income countries and countries with poor science funding it is very di cult to incorporate that kind of training at different stages of scientist research career (Moore et al, 2021). This is just one of multiple reasons why many open-access databases were and are still underutilized and reserved only for laboratories that have people with adequate programming expertise (Akil et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

NeuroMorpho Access Tool: A Simple GUI for Accessing NeuroMorpho.Org Database

Zaletel

Vidaković²,

Nowakowski

2022

Preprint

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The use of open-access data has become increasingly prevalent in modern neuroscience research. These data are commonly used as a supplement to practical experimental research, but there is also an increasing body of literature which relies exclusively on the use of such publicly available data. Although freely available, these databases usually require an adequate level of training in bioinformatics and/or programming for a researcher to access them, which limits their usability. One of the oldest, most utilized and maintained databases of neuron and glia cell morphology is the NeuroMorpho.Org database, which can be access through the use of application programing interface (API). In the present paper we introduce the NeuroMorpho Access Tool (NMAT), a simple and user-friendly graphical user interface (GUI) program, which allows easy and fast access to the NeuroMorpho.Org database to any neuroscientist, regardless of their previous bioinformatics knowledge. The core of NMAT was built in Python, utilizes the NeuroMorpho.Org API in order access the database, and has a GUI built in Qt environment. The program is lightweight, consists of only one executable file and does not require any extensive accompanying instructional or technical documentation. The current version of the program enables the users to obtain cell reconstruction data together with morphometry data and also acquire images of cell reconstructions. The main advantage of NMAT is its multithreading capability, which allows the users to gain access to a large amount of data in a very short time period. Thus, NMAT may prove as a usefully tool which would complement the highly utilized NeuroMorpho.Org database.

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Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Cited by 9 publications

References 22 publications

Brazilian women in Bioinformatics: Challenges and opportunities

Brazilian women in Bioinformatics: Challenges and opportunities

Bridging the gap in African biodiversity genomics and bioinformatics

NeuroMorpho Access Tool: A Simple GUI for Accessing NeuroMorpho.Org Database

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