User talk:Hiram
ISMB 2008, Toronto Ontario Canada
Metagenomics approaches
1: Science. 2006 Jun 2;312(5778):1355-9
Metagenomic analysis of the human distal gut microbiome.
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS,
Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE.
| Fraser-Liggett
Estimating True Evolutionary Distances uunder the DCJ Model
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/13/i114
Estimating true evolutionary distances under the DCJ model
Yu Lin and Bernard M.E. Moret
Laboratory for Computational Biology and Bioinformatics,
Swiss Federal Institute of Technology (EPFL), EPFL-IIS-LCBB,
INJ 230, Station 14, CH-1015 Lausanne, Switzerland
Mail list concerning the big data management from the new sequencing technologies: bioinfo-core
VisANT - pathway visualization tool
comments
- hm... thinking Gangleri 12:46, 7 April 2006 (PDT)
- copying this code and making a preview at a Wikimedia foundation wiki ...
- both variants will work; please tray to find out what Tidy is; where you can download ond how you can install it; I never operated a wiki myself but I did a lot of tests; I understand that Tidy is a kind of wizzard correcting HTML code / generating errorfree HTML code
- note: commons:wikt:yi:user:Gangleri/tests/bugzilla#test wiki's lists a lot of test wikies; if you make a preview at [1] you will see that there the behaviour is the same as here; please do not get angry; I was searching the answer for months
- Good luck! You can reach me on the IRC-channel #wiktionary or skype me 'irelgnag'. Best regards Gangleri 13:04, 7 April 2006 (PDT)
Special:Confirmemail does either not work or is / might be delayed.Best regards Gangleri · T · m: Th · T 13:17, 7 April 2006 (PDT)
Genomics and Justice - 2007-05-18
What is important and want to carry forward from session to session
What are important but need to be backgrounded
what do we know
Morning session, 09:30
Participatory forms
What are the underlying concepts of Justice when a particular "performance" is seen in a public forum. Can you perhaps have a philosophical advisory team on the side to provide a checks and balance function and provide advice to questions of justice as they come up in a research situation.
Example from Tuscan Italy experience, don't mince words when asking for samples, make it clear that samples are needed to help with the research. Offer an exchange of something valuable for the samples. Doesn't do much good to try and promote some kind of community wide involvement as if you were passing off responsibility to that "group". The researcher has to have enough guts to realize they will continue to have the responsibility no matter how much the group has been informed about the research.
Property
Public domain, collective commons. Copyleft. Foster innovation in complete openness by doing innovation in public. Against what do we need to secure the open access for this new set of biological information. "Creative commons is not communism." Illicit copies. The "generic" can only exist if the private patented item exists. Given definitional terms, it is only possible to have public domain commons if and only if there exists a private domain for that same business.
Patent system - one mechanism of answering the question of how to get innovation to happen. This avoids the problem of how do these innovations become applied to the actual problems that exist.
The benefits of the public domain. It can solve problems that markets do not care about. For example the knowledge of smoking is dangerous, was in the public domain in the 1950s and was alleviated by behavioral changes. Penicillin development has an interesting history. Interesting problems can be solved efficiently by taking public domain knowledge, turning it into a private resource which then makes it valuable and will become available.
Groups without power have notions of identity and property that need to be protected when external forces walk in and have different ideas of identity and property.
Sovereignty
Aboriginal title, rights of occupancy, what native peoples have. What is present in native culture, definitions, meanings, stories, how do they fit into the structures being imposed upon them. DNA on "loan" contracts.
Test Custom Track Link
Custom track: Hg18 small exons and introns on the UCSC Genes track
Rat Genome Meeting CSHL 09 Dec 2007
new assembly due about end of Jan 2008
cDNAs being worked on from other strains.
Perhaps about 4,000 to 5,000 EuraTools
Sequencing other strains, brown norway on 454 to 4X end of 2008, maybe whole genome, depends upon technology.
Check with the Japan folks, they've been doing BAC ENDs on two rats. The data is in trace archives by about April.
Baylor is currently working on SNP calls, want one set, no dups please, about 8 strins, perhaps several million, trouble with how far apart the strains are.
sequencing, or sampling, other strains, best to improve QTL, don't worry about the exons.
the SHR strain may be done with the Solexa procedure if paired end protocol can work. Might be $30K Canadian for a Solexa run at 3X coverage.
need list of strains and the relative value in their sampling/sequencing.
Ewan proposes RGD identifiers as the primary naming, certainly xref to the others. Should there be an RGD id for all gene models ? Trouble is when things disappear. The idea is to have as much as possible. Beware of naming schemes that are too tenative to begin with.
Entrez genes, Ensembl
request to have all the genes done by Sept.
coordinate between Ensembl, RGD and UCSC to cull the best coincident predictions, and have something to say about the differences.
Ontologies at RGD -
Mary Shimoyama
Gene Ontology
Mammalian Phenotype Ontology - developed at MGD
Pathway Ontology - developed at RGD
Disease
Behavior
Rat genes with GO 17,000
Trying to keep up with GO on a weekly basis
Ewan suggests that strain names are used only if they are in the RGD Strain Ontology DB
There is a big Mouse ontology meeting in Europe every year, good to coordinate with them. Euro Phemone
eQTL tracks are new to Ensembl available via the DAS source menus in about a week.
Ewan would like UCSC to be DAS clients.
Can the Rat folks agree on a set of cell lines to use for genome-wide surveys ? Do rat folks think of genome-wide surveys ?
Next Rat meeting like this next year in Hinxton. Then 2009 CSHL again.
Top 10 items to worry about
It is important to keep your list straight when worrying about things. A proper perspective needs to be considered at all times.
- fresh water supply
- USA public debt
- global warming
- mono-culture crop and livestock strains
- population stress exacerbates all other problems
- the end of oil
- billions of refugees wandering about looking for food and water
- declining fish populations
- antibotic resistant bacterial infections
Links to remember
NY Times 2007-06-29 The Cult of the Amateur, By MICHIKO KAKUTANI, Published: June 29, 2007
