The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Eleni Giannoulatou - One of the best experts on this subject based on the ideXlab platform.

  • How to test Bioinformatics Software?
    Biophysical Reviews, 2015
    Co-Authors: Amir Hossein Kamali, Eleni Giannoulatou, Tsong Yueh Chen, Michael A. Charleston, Alistair L. Mcewan, Joshua W. K. Ho
    Abstract:

    Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific Software, but very few studies have directly dealt with the issues of Bioinformatics Software testing. In this work, we review important concepts and state-of-the-art methods in the field of Software testing. We also discuss recent reports on adapting and implementing Software testing methodologies in the Bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

  • verification and validation of Bioinformatics Software without a gold standard a case study of bwa and bowtie
    BMC Bioinformatics, 2014
    Co-Authors: Eleni Giannoulatou, Shinho Park, David T Humphreys
    Abstract:

    Bioinformatics Software quality assurance is essential in genomic medicine. Systematic verification and validation of Bioinformatics Software is difficult because it is often not possible to obtain a realistic "gold standard" for systematic evaluation. Here we apply a technique that originates from the Software testing literature, namely Metamorphic Testing (MT), to systematically test three widely used short-read sequence alignment programs. MT alleviates the problems associated with the lack of gold standard by checking that the results from multiple executions of a program satisfy a set of expected or desirable properties that can be derived from the Software specification or user expectations. We tested BWA, Bowtie and Bowtie2 using simulated data and one HapMap dataset. It is interesting to observe that multiple executions of the same aligner using slightly modified input FASTQ sequence file, such as after randomly re-ordering of the reads, may affect alignment results. Furthermore, we found that the list of variant calls can be affected unless strict quality control is applied during variant calling. Thorough testing of Bioinformatics Software is important in delivering clinical genomic medicine. This paper demonstrates a different framework to test a program that involves checking its properties, thus greatly expanding the number and repertoire of test cases we can apply in practice.

David T Humphreys - One of the best experts on this subject based on the ideXlab platform.

  • verification and validation of Bioinformatics Software without a gold standard a case study of bwa and bowtie
    BMC Bioinformatics, 2014
    Co-Authors: Eleni Giannoulatou, Shinho Park, David T Humphreys
    Abstract:

    Bioinformatics Software quality assurance is essential in genomic medicine. Systematic verification and validation of Bioinformatics Software is difficult because it is often not possible to obtain a realistic "gold standard" for systematic evaluation. Here we apply a technique that originates from the Software testing literature, namely Metamorphic Testing (MT), to systematically test three widely used short-read sequence alignment programs. MT alleviates the problems associated with the lack of gold standard by checking that the results from multiple executions of a program satisfy a set of expected or desirable properties that can be derived from the Software specification or user expectations. We tested BWA, Bowtie and Bowtie2 using simulated data and one HapMap dataset. It is interesting to observe that multiple executions of the same aligner using slightly modified input FASTQ sequence file, such as after randomly re-ordering of the reads, may affect alignment results. Furthermore, we found that the list of variant calls can be affected unless strict quality control is applied during variant calling. Thorough testing of Bioinformatics Software is important in delivering clinical genomic medicine. This paper demonstrates a different framework to test a program that involves checking its properties, thus greatly expanding the number and repertoire of test cases we can apply in practice.

Abdoulaye Banire Diallo - One of the best experts on this subject based on the ideXlab platform.

  • a novel comprehensive wheat mirna database including related Bioinformatics Software
    Current Plant Biology, 2016
    Co-Authors: Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A Badawi, Fathey Sarhan, Abdoulaye Banire Diallo
    Abstract:

    Abstract MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators that may regulate key genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, including in silico predicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction Software tuned to de novo miRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and Software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web portal is available at: http://wheat.bioinfo.uqam.ca .

  • wmp a novel comprehensive wheat mirna database including related Bioinformatics Software
    bioRxiv, 2015
    Co-Authors: Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A Badawi, Fathey Sarhan, Vladirmir Makarenkov, Abdoulaye Banire Diallo
    Abstract:

    MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators that may regulate key plant genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, including in silico predicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction Software tuned to de novo miRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and Software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web-portal is available at: http://wheat.bioinfo.uqam.ca.

Chaogang Shao - One of the best experts on this subject based on the ideXlab platform.

  • srnatargetdigger a Bioinformatics Software for bidirectional identification of srna target pairs with co regulatory srnas information
    PLOS ONE, 2020
    Co-Authors: Zhihong Yang, Yeqin Jiang, Rongkai Guo, Yijun Meng, Chaogang Shao
    Abstract:

    Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many Bioinformatics Software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining Software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining Software, sRNATargetDigger, that includes two function modules, “Forward Digger” and “Reverse Digger”, which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This Software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.

Mickael Leclercq - One of the best experts on this subject based on the ideXlab platform.

  • a novel comprehensive wheat mirna database including related Bioinformatics Software
    Current Plant Biology, 2016
    Co-Authors: Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A Badawi, Fathey Sarhan, Abdoulaye Banire Diallo
    Abstract:

    Abstract MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators that may regulate key genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, including in silico predicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction Software tuned to de novo miRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and Software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web portal is available at: http://wheat.bioinfo.uqam.ca .

  • wmp a novel comprehensive wheat mirna database including related Bioinformatics Software
    bioRxiv, 2015
    Co-Authors: Mohamed Amine Remita, Etienne Lord, Zahra Agharbaoui, Mickael Leclercq, Mohamed A Badawi, Fathey Sarhan, Vladirmir Makarenkov, Abdoulaye Banire Diallo
    Abstract:

    MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators that may regulate key plant genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, including in silico predicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction Software tuned to de novo miRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and Software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web-portal is available at: http://wheat.bioinfo.uqam.ca.