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Articles 1 - 9 of 9
Full-Text Articles in Life Sciences
Biol 4010w/7190g/Cisc2810w: Macromolecular Structure And Bioinformatics, Shaneen Singh
Biol 4010w/7190g/Cisc2810w: Macromolecular Structure And Bioinformatics, Shaneen Singh
Open Educational Resources
No abstract provided.
Biomedical Informatics Colloquium, Bio 4050, Course Outline, Eugenia G. Giannopoulou
Biomedical Informatics Colloquium, Bio 4050, Course Outline, Eugenia G. Giannopoulou
Open Educational Resources
A seminar-based course that exposes students to current research topics in the fields of Bioinformatics and Medical Informatics. Weekly presentations by invited speakers and/or faculty introduce students to the broad diversity of research areas in both fields, and engages them in critical thinking and writing. Online lectures and reading activities will be given periodically.
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.
Bioinformatics Ii, Bio 3352, Course Outline, Eugenia G. Giannopoulou
Bioinformatics Ii, Bio 3352, Course Outline, Eugenia G. Giannopoulou
Open Educational Resources
This course is a continuation of Bioinformatics I. Topics include gene expression, microarrays, next- generation sequencing methods, RNA-seq, large genomic projects, protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; and protein-nucleic acid interactions. The lab component includes R-based statistical data analysis on large datasets, introduction to big data analysis tools, protein visualization software, internet-based tools and high-level programming languages.
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.
Natural Resources Biometrics, Diane Kiernan
Natural Resources Biometrics, Diane Kiernan
Open Educational Resources
Natural Resources Biometrics is a peer reviewed open textbook that begins with a review of descriptive statistics, estimation, and hypothesis testing. The following chapters cover one- and two-way analysis of variance (ANOVA), including multiple comparison methods and interaction assessment, with a strong emphasis on application and interpretation. Simple and multiple linear regressions in a natural resource setting are covered in the next chapters, focusing on correlation, model fitting, residual analysis, and confidence and prediction intervals. The final chapters cover growth and yield models, volume and biomass equations, site index curves, competition indices, importance values, and measures of species diversity, association, …