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Welcome to the Bioinfotropes Wiki

Bioinfotropes is a collection of patterns, paradigms, and concepts for guiding new discoveries in systems biology and building better descriptions of familiar systems. Common themes in the evolutionary behavior of systems biology, in the observed behaviors of various bioinformatics tools and approaches, in rationales for rule-based annotation and hypothesis generation, and in emerging descriptive frameworks from the bioinformatics literature are discussed here. The coinage "Bioinfotropes" pays tribute to TV Tropes, a cataloguing of literary devices and conventions that writers can predict will resonate with the expectations and experience of their audiences.

Listed Bioinfotropes

Anna Karenina principle for microbiomes

annotation walking

bioinformatics grammar

bioinformatics journey

cofactor dependency signature

codon tricks

dedicated system

divergon

edge piece for system reconstruction

equivalog

fitness factors a.k.a. lysogenic conversion genes, "morons"

genetic logic circuits

Genome Properties and SEED Subsystems

guild of protein families

lab weeds

misannotation's greatest hits

mix-and-match association

neofunctionalization

non-orthologous gene displacement

one-gene system

orphan marker

phylogenetic footprinting (contribution invited)

protein sorting system

recurring pathway hole

sequence gazing

sporadic distribution

sugar utilization pathway

uniform functional organization

upstream and auxiliary components

History and Support

Bioinfotropes was founded in November 2010 by Daniel Haft, an Assistant Professor at the J. Craig Venter Institute, as a means to create vocabularies through which experts in bioinformatics can more easily communicate their findings and methods. It is also intended to serve as resource that will enhance community development of rule-based annotation. This project abstracts a number of advances in bioinformatics in which the logic of the approach exploits special characteristics of the class of system under study. Bioinfotropes includes discussions of recent and on-going work supported by grant R01 HG004881 from NIH/NHGRI, but enthusiastically invites all scholarly contributions that fit the open spirit of the project.

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