Difference between revisions of "Informal programming"
(Created page with "<div id="APB"> <div class="b1"> "Informal" programming </div> {{dev}} Much of our programming work is "informal" in the sense that - simply for reasons of practicality - i...") |
m (→Development) |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 12: | Line 12: | ||
__TOC__ | __TOC__ | ||
| + | |||
| + | |||
| + | ==Introductory reading== | ||
| + | <section begin=reading /> | ||
| + | <div class="reference-box">[http://software-carpentry.org/articles/how-scientists-use-computers-2009.pdf How scientists use computers] (PDF at software-carpentry.org)</div> | ||
| + | <section end=reading /> | ||
| Line 21: | Line 27: | ||
* (-) one-off tasks | * (-) one-off tasks | ||
* (+) agile | * (+) agile | ||
| − | |||
==Development== | ==Development== | ||
| − | |||
| + | * scripting vs. compiling | ||
| + | * Perl | ||
| + | * Python | ||
| + | * PHP | ||
| + | * The LAMP stack | ||
==Documentation== | ==Documentation== | ||
| Line 35: | Line 44: | ||
... | ... | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| Line 49: | Line 53: | ||
==References== | ==References== | ||
<references /> | <references /> | ||
| − | |||
| − | |||
| Line 56: | Line 58: | ||
==Further reading and resources== | ==Further reading and resources== | ||
| + | {{#pmid: 18287711}} | ||
| + | {{#pmid: 21370093}} | ||
| + | <div class="reference-box">[http://software-carpentry.org/ The '''Software Carpentry''' project] based on the excellent course and other activities of Greg Wilson at UofT and elsewhere.</div> | ||
| Line 62: | Line 67: | ||
</div> | </div> | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 11:57, 27 January 2012
"Informal" programming
Much of our programming work is "informal" in the sense that - simply for reasons of practicality - it does not respect the well-established paradigms of software engineering. Some sources refer to end-user programming to contrast this with programming by developers. Here we discuss parameters of such informal programming and how to avoid a number of potential problems.
Contents
Introductory reading
Parameters
- (+) domain knowledge
- (-) knowledge of tools, theory, and best practices
- (-) infrequent tasks
- (-) one-off tasks
- (+) agile
Development
- scripting vs. compiling
- Perl
- Python
- PHP
- The LAMP stack
Documentation
...
Testing
...
Exercises
References
Further reading and resources
| Stajich (2007) An Introduction to BioPerl. Methods Mol Biol 406:535-48. (pmid: 18287711) |
|
[ PubMed ] [ DOI ] The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. |
| Mühlberger et al. (2011) Computational analysis workflows for Omics data interpretation. Methods Mol Biol 719:379-97. (pmid: 21370093) |
|
[ PubMed ] [ DOI ] Progress in experimental procedures has led to rapid availability of Omics profiles. Various open-access as well as commercial tools have been developed for storage, analysis, and interpretation of transcriptomics, proteomics, and metabolomics data. Generally, major analysis steps include data storage, retrieval, preprocessing, and normalization, followed by identification of differentially expressed features, functional annotation on the level of biological processes and molecular pathways, as well as interpretation of gene lists in the context of protein-protein interaction networks. In this chapter, we discuss a sequential transcriptomics data analysis workflow utilizing open-source tools, specifically exemplified on a gene expression dataset on familial hypercholesterolemia. |
