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Full-Text Articles in Life Sciences
Deep Machine Learning Techniques For The Detection And Classification Of Sperm Whale Bioacoustics, Peter C. Bermant, Michael M. Bronstein, Robert J. Wood, Shane Gero, David F. Gruber
Deep Machine Learning Techniques For The Detection And Classification Of Sperm Whale Bioacoustics, Peter C. Bermant, Michael M. Bronstein, Robert J. Wood, Shane Gero, David F. Gruber
Publications and Research
We implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract finer-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classification tasks, including (1) …
Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim
Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim
Open Educational Resources
This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.
Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim
Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim
Open Educational Resources
This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.
Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim
Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim
Open Educational Resources
This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the …
Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim
Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim
Open Educational Resources
This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.
Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim
Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim
Open Educational Resources
This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.