Building a local web application with Flask
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Flask is a microframework for Python web development that makes it easy to build web applications. It helps separate Python code from HTML templates, generates RESTful URLs, and has a flexible MVC design pattern. Flask applications can be used to summarize and share information, promote research, and blog. The documentation for Flask and its templating engine Jinja2 is very good.
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Wade Kariniemi is seeking an internship in computer science and has experience in web development, programming languages like Java and JavaScript, and customer service. He has worked as a developer for Zigmens automating workflows using AppScript and building websites. Kariniemi also has experience in web sales management and hardware installation. He is currently a junior studying computer science at Arizona State University.
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BioRender & Glossary/Acronym
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Linters in R
Linters in R provides a 3 sentence summary of the document:
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BioSyntax: syntax highlighting for computational biology
bioSyntax is syntax highlighting software for computational biology. It highlights nucleotides, amino acids, and quality scores in common file formats used in bioinformatics like FASTA, FASTQ, SAM, BAM, VCF, GTF and custom formats. bioSyntax works in many text editors and terminals to help visualize and interpret genomic data. It supports common color schemes and allows customizing colors for specific nucleotides, amino acids or quality scores to highlight features of interest in sequences and alignments.
Get Good With Git
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MultiQC: summarize analysis results for multiple tools and samples in a singl...
MultiQC is a tool that aggregates bioinformatics quality control (QC) results from different tools into a single HTML report. It currently supports 73 tools and can integrate QC metrics from preprocessing, alignment, and post-alignment stages. MultiQC generates interactive plots and tables in an customizable report to allow users to compare QC metrics across multiple samples and tools in an flexible manner.
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Efficient querying of genomic reference databases with gget
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BioSyntax: syntax highlighting for computational biology
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- 1. Building a local web application with Flask Mickaël Mendez - Tech Talk - December 21, 2016
- 2. Why would you develop a web application ? ● Main goal: Summarize and Display information ● Share results with collaborators ● Promote your research ● Blogging ● Why not? Python makes it very easy!
- 3. What not to do ● Don’t write html tags within your Python script. It will become impossible to read as the project grows ● Don’t write URLs manually. It requires unnecessary engineering to keep track of the current location and format the links properly
- 4. Some Numbers ● 800 Lines of Code ● 450 Lines of Code ● 1500 Lines of Code (Test) ● 1000 Lines of Code (Test) ● 200 A4 pages of Documentation ● 140 A4 pages of Documentation 2011-2015
- 5. Instead use Flask ● Micro-framework for Python web development ● RESTful URL mapping ● Contains development server and debugger ● Flexible MVC design pattern (Jinja2) ● Very good documentation
- 6. Hello World
- 7. Hello World
- 9. Templates
- 10. Templates (Jinja2) For loops If statements
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- 12. Template inheritance Child: templates/hello.tpl Parent: templates/layout.tpl
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- 15. Good links Flask4scientists: http://hplgit.github.io/web4sciapps/doc/pub/web4sa_solarized.html Flask Documentation: http://flask.pocoo.org/docs/0.11/ Jinja2 Documentation: http://jinja.pocoo.org/docs/dev/
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