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<strong>MediaWiki has been installed.</strong>
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Welcome to biowiki.org, an online notebook for [[Holmes Lab|Ian Holmes' research group]] at the University of California, Berkeley.
  
Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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= About =
  
== Getting started ==
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Information about the group.
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
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== People ==
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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* [[Holmes Lab|Holmes lab]] members
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
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** PhD: [[Jordi Silvestre Ryan]]
 +
** Programmer: [[Eric Yao]]
 +
** PI: [[Ian Holmes]]
 +
 
 +
== Location ==
 +
 
 +
* Address: 381 [[Stanley Hall]], University of California, Berkeley, CA 94720-3220.
 +
* Phone: (510) 666 - 2791.
 +
 
 +
== Papers ==
 +
 
 +
* [[Paper Archive|List of published papers]]
 +
 
 +
= Software =
 +
 
 +
Links to software developed by the group.
 +
 
 +
== Genome informatics ==
 +
 
 +
=== JBrowse ===
 +
 
 +
[https://jbrowse.org/ JBrowse] is a JavaScript genome browser.
 +
Fast, portable, and secure, it's used by thousands of sites including a large number of model organism projects.
 +
 
 +
* {{#pmid:27072794}}
 +
 
 +
[http://genomearchitect.org/ Apollo], the online curation platform, is built on top of JBrowse:
 +
 
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* {{#pmid:24000942}}
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=== Biomake ===
 +
 
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[http://biomake.org Biomake] is a port of GNU Make that allows MD5 signatures, job submission to queues, multiple wildcards per rule, and logic programming extensions.
 +
 
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* Holmes IH & Mungall CJ. 2016. [http://biorxiv.org/content/early/2016/12/12/093245 BioMake: a GNU Make-compatible utility for declarative workflow management.]
 +
 
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== Molecular evolution ==
 +
 
 +
=== Historian ===
 +
 
 +
[https://github.com/evoldoers/historian Historian] is a program for ancestral sequence reconstruction, using phylogenetic Markov chain models of substitutions and indels.
 +
In our tests (as of 2016) it's the most accurate tool for reconstructing ancient sequences and rates.
 +
 
 +
* Holmes, IH. 2016. [http://biorxiv.org/content/early/2016/12/11/093161 Historian: accurate reconstruction of ancestral sequences and evolutionary rates.]
 +
 
 +
=== XRate ===
 +
 
 +
[[Xrate Software|xrate]] is software for fitting structured phylogenetic models to multiple sequence alignments.
 +
It's been used to estimate many substitution models, including these ones:
 +
* {{#pmid:18367465}}
 +
* {{#pmid:17400572}}
 +
* {{#pmid:23188590}}
 +
 
 +
It can also be used to fit structured phylogenetic grammars to multiple alignments, e.g. as described here:
 +
* {{#pmid:22693624}}
 +
* {{#pmid:19668382}}
 +
 
 +
And it can do ancestral sequence reconstruction:
 +
* {{#pmid:26186661}}
 +
 
 +
Some more links:
 +
* [[Xrate Tutorial|Tutorial]] on using xrate
 +
* [[Phylo Grammars|Background]] on phylogenetic grammars
 +
* [[Xrate Format|xrate format]] - documentation of the xrate model format
 +
 
 +
=== Stemloc ===
 +
 
 +
[[Stem Loc|stemloc]] is software for simultaneous alignment and folding of RNA.
 +
* {{#pmid:15790387}}
 +
* {{#pmid:18796475}}
 +
 
 +
== Other bioinformatics tools ==
 +
 
 +
=== File formats ===
 +
 
 +
The lab provides several tools for manipulating standard bioinformatics file formats:
 +
 
 +
* [[Stockholm Tools]] for working with the Stockholm format
 +
* [[Gff Tools]] for working with the GFF format
 +
 
 +
=== DNA storage ===
 +
 
 +
[https://github.com/ihh/dnastore dnastore] is software for encoding and decoding information in DNA sequences using error-tolerant codes that are robust to insertions, deletions and duplications
 +
* Holmes, 2016. [https://arxiv.org/abs/1606.01799 Modular non-repeating codes for DNA storage]
 +
 
 +
=== Gene ontology ===
 +
 
 +
[https://github.com/ihh/wtfgenes wtfgenes] is software implementing the MCMC method of Bauer _et al_ for gene set analysis using the [[Gene Ontology]]
 +
* {{#pmid:20172960}}
 +
 
 +
=== Oxford nanopore ===
 +
 
 +
[https://github.com/ihh/quaff quaff] is a Pair HMM for aligning [[Oxford nanopore]] reads.
 +
 
 +
== Non-bioinformatics tools ==
 +
 
 +
=== ASCII art ===
 +
 
 +
[https://github.com/ihh/figlet-js figlet-js] is a JavaScript implementation of figlet by Scott Gonzalez. We have added to it some animation effects and an interactive demo.
 +
* [https://biowiki.org/wiki/extensions/Figlet/figlet-js/ Demo]
 +
* [https://github.com/ihh/figlet-js Source code]
 +
 
 +
=== Procedural graphics ===
 +
 
 +
[https://github.com/ihh/facesjs facesjs] is a JavaScript library by Jeremy Scheff for generating vector-based cartoon faces. We have added to the facial feature repertoire and included some basic affect modeling.
 +
* [http://biskup.biowiki.org/facesjs/ Demo]
 +
* [https://github.com/ihh/facesjs Source code]
 +
 
 +
=== Interactive fiction ===
 +
 
 +
[http://biskup.biowiki.org/boswell/ Boswell] is an experimental IDE for authoring and hosting multi-player choice-based interactive fiction.
 +
* [http://biskup.biowiki.org/boswell/ Demo]
 +
* [https://github.com/ihh/boswell/ Source code]
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* Holmes, 2014. [https://github.com/ihh/boswell/blob/master/doc/latex/lwpaper.pdf A Web-Based Editor for Multiplayer Choice Games.] Proceedings of the 9th International Conference on the Foundations of Digital Games.
 +
 
 +
=== Wiki migration ===
 +
 
 +
This wiki was hosted for many years using [http://twiki.org/ TWiki]. For various mundane reasons we eventually moved it to [https://www.mediawiki.org/ Mediawiki]. To do this we modified a script originally written by Ryan Castillo. Our updated version of this script is linked below.
 +
* [https://github.com/ihh/Twiki-to-Mediawiki Source code]
 +
 
 +
= Writing =
 +
 
 +
Random rants on this wiki.
 +
 
 +
== Essays on algorithms and applications ==
 +
* [[String Transducers]]: finite state machines for molecular evolution
 +
* [[Stochastic Grammars]]
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* [[Phylogenetic Alignment]]
 +
 
 +
== Collections of links to papers ==
 +
* [[Transposon Papers]]: bioinformatic annotation of transposons
 +
* [[Phylogenetic Alignment Reader]]: multiple alignment with evolutionary models
 +
* [[Nucleic Acid Engineering]]: synthetic DNA & RNA machines
 +
 
 +
== Teaching pages ==
 +
* [[Cryptanalysis Exercises]]
 +
* [[Unix Tutorial]]
 +
 
 +
== Opinion pieces ==
 +
* [[Genome Wiki]]
 +
* [[Makefile Manifesto]]
 +
* [[File Format Design]]

Latest revision as of 17:25, 5 January 2017

Welcome to biowiki.org, an online notebook for Ian Holmes' research group at the University of California, Berkeley.

About

Information about the group.

People

Location

  • Address: 381 Stanley Hall, University of California, Berkeley, CA 94720-3220.
  • Phone: (510) 666 - 2791.

Papers

Software

Links to software developed by the group.

Genome informatics

JBrowse

JBrowse is a JavaScript genome browser. Fast, portable, and secure, it's used by thousands of sites including a large number of model organism projects.

Apollo, the online curation platform, is built on top of JBrowse:

Biomake

Biomake is a port of GNU Make that allows MD5 signatures, job submission to queues, multiple wildcards per rule, and logic programming extensions.

Molecular evolution

Historian

Historian is a program for ancestral sequence reconstruction, using phylogenetic Markov chain models of substitutions and indels. In our tests (as of 2016) it's the most accurate tool for reconstructing ancient sequences and rates.

XRate

xrate is software for fitting structured phylogenetic models to multiple sequence alignments. It's been used to estimate many substitution models, including these ones:

It can also be used to fit structured phylogenetic grammars to multiple alignments, e.g. as described here:

And it can do ancestral sequence reconstruction:

Some more links:

Stemloc

stemloc is software for simultaneous alignment and folding of RNA.

Other bioinformatics tools

File formats

The lab provides several tools for manipulating standard bioinformatics file formats:

DNA storage

dnastore is software for encoding and decoding information in DNA sequences using error-tolerant codes that are robust to insertions, deletions and duplications

Gene ontology

wtfgenes is software implementing the MCMC method of Bauer _et al_ for gene set analysis using the Gene Ontology

Oxford nanopore

quaff is a Pair HMM for aligning Oxford nanopore reads.

Non-bioinformatics tools

ASCII art

figlet-js is a JavaScript implementation of figlet by Scott Gonzalez. We have added to it some animation effects and an interactive demo.

Procedural graphics

facesjs is a JavaScript library by Jeremy Scheff for generating vector-based cartoon faces. We have added to the facial feature repertoire and included some basic affect modeling.

Interactive fiction

Boswell is an experimental IDE for authoring and hosting multi-player choice-based interactive fiction.

Wiki migration

This wiki was hosted for many years using TWiki. For various mundane reasons we eventually moved it to Mediawiki. To do this we modified a script originally written by Ryan Castillo. Our updated version of this script is linked below.

Writing

Random rants on this wiki.

Essays on algorithms and applications

Collections of links to papers

Teaching pages

Opinion pieces