<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38489?offset=210 https://bioinformaticsonline.com/bookmarks/view/39190/chipulate-a-python3-framework-to-simulate-read-counts-in-a-chip-seq-experiment Mon, 25 Mar 2019 12:46:47 -0500 https://bioinformaticsonline.com/bookmarks/view/39190/chipulate-a-python3-framework-to-simulate-read-counts-in-a-chip-seq-experiment <![CDATA[ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment]]> ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number of replicates needed to confidently infer binding strength.

Address of the bookmark: https://github.com/vishakad/chipulate

]]> Abhimanyu Singh https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources Tue, 28 Jun 2022 07:32:05 -0500 https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources <![CDATA[Finding a mimicry game for teaching on-line and mentioned general resources]]> Mimicry and other resources Mimicry games: Great Heliconius game: http://heliconius.org/evolving_butterflies/ (See also https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014) Other one, a bit less friendly: https://ccl.northwestern.edu/netlogo/models/Mimicry Camouflage practical https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/ (NetLogo also has one: https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage) Peppered moth game: https://askabiologist.asu.edu/peppered-moths-game/play.html General resources The always popular Populus: https://cbs.umn.edu/populus/overview Drift & Gene Flow https://cartwrig.ht/apps/genie/ (Cock van Oosterhout has a great ppt to lead students through this) See also https://cartwrig.ht/apps/redlynx/ https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/ NetLogo: http://ccl.northwestern.edu/netlogo/models/index.cgi Population Genetics: https://www.radford.edu/~rsheehy/Gen_flash/popgen/ Evolution in general https://evolution.berkeley.edu/evolibrary/home.php Mitochondrial Eve: https://projects.ncsu.edu/cals/gn/ex/mit-eve.html Y chromosomes: https://projects.ncsu.edu/cals/gn/ex/y-chrom.html A professional online package from Michael Kasumovic: https://arludo.com/ a compilation of resources: https://planted.botany.org/index.php?P=Home Finally, Donald Forsdyke has some great on-line videos explaining evolutionary principles (occasionally in a fake Scottish accent): http://post.queensu.ca/~forsdyke/videolectures.htm

 

]]> Shruti Paniwala