Xenopus Community

XenCommunity

Under Construction. Edits and suggestions welcome.

• See Synthetic Biology Community Pages for ideas.
• Edit help for this section or to make your own lab wiki
• Editing is easy with wiki edit instructions.
• It was a wonderful meeting in Japan, especially the meeting summary given by Jerry.

Discussion about having XenWiki on OWW or hosted at [XenBase]

• XenBase could set up and host a wiki for the Xen Community on its new server, or the XenWiki could be here on OWW. I justed added a few thoughts.

Advantages to hosting XenWiki on OWW

• general reasons to join OWW

1. Broader involvement with the non-Xenopus scientific community
2. Xen Labs will learn about other work going on in OWW labs, esp. Synthetic Biology
3. OWW has a lab-tweaked mediawiki
4. very interactive scientists with many interests are managing the OWW site
5. learning curve for wikitricks (editing, etc) is very good because of all the help and organization on OWW. This will help new XenLabs get wikified.
6. don't have to cope with administrative and technical overhead of setting up/maintaining the software and hardware to run the wiki
7. backed up every day -> moving to server with redundant hardware, diesel power backup, multiple server uplinks to internet, 1 hr hardware replacement guarantee, 24hr monitoring... et cetera
8. it does not hurt to try, and then move your wiki later. As long as you are using mediawiki (by far the largest wiki distribution), you can always move pages later. It really is just copying and pasting code. In fact, we could probably export the whole lot for you.

Advantages to hosting XenWiki through the [XenBase] server

1. direct links possible between Xenwiki and XenBase areas
   • this is possible (and probably easier) on OWW as we have experience with other databases (BioBricks), and could probably easily modify it to contain your information.
2. control
3. private spaces -> one could implement a scheme (not technically possible yet, but could be programmed in) where individual pages have different rights. Essentially, giving users the ability to place read/write controls on data.

Discuss and decide what we need so we can ask NIH, get involved with NIH "report" recommendations

• notes from 11th Xen Meeting: Instructions for submitting a proposal NHGRC: see 'white paper' instructions on web site (need the link)
• program announcement due Jan 18 2007, document on web site but applications that do the best produce a resource for the community and also do good science, US labs and non-US labs are considered.

Next Meeting

• will be in Germany, details TBA
• contact committee for ideas for next meeting

Collected from Bruce Blumberg's excellent Xine

• Xenopus Tutorial from Amy Sater
• 1050-marker genetic map for X. tropicalis

Xine in html format, back issues

• [1]
• [2]
• [3]

Links to useful sources of information for Xenopus (in no particular order) general interest and utility

• Trans NIH Xenopus initiative
• Harland lab X. tropicalis site
• Grainger lab X. tropicalis site
• Amy Sater's X. tropicalis genetic map site
• Information on the X. tropicalis listserver
• Peter Vize's Xenopus über database
• Zimmerman Lab X. tropicalis website, database of mutants
• metazome

Genomic resources

• XDB at NIBB - Naoto Ueno's X. laevis EST database
• Xenopus gene collection
• full length collection at the Gurdon Institute
• JGI X. tropicalis genome site with browser and other info
• AXELDB - Christof Niehrs' Xenopus database
• Xenbase

Other

• The Frog Store Isn't the internet wonderful?

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Recent changes

List of abbreviations:

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23 March 2019

			07:51		Schumer lab: Commonly used workflows‎‎ (7 changes | history) . . (+5,797)‎ . . [Schumer‎ (7×)]
					07:51 (cur | prev) . . (+56)‎ . . Schumer (talk | contribs)
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					05:37 (cur | prev) . . (+1)‎ . . Schumer (talk | contribs) (→‎Merging multiple ancestry tsv files run separately)
					05:37 (cur | prev) . . (+10)‎ . . Schumer (talk | contribs) (→‎Merging multiple ancestry tsv files run separately)
					05:36 (cur | prev) . . (+5,356)‎ . . Schumer (talk | contribs) (→‎Merging multiple ancestry tsv files run separately)
					04:54 (cur | prev) . . (+272)‎ . . Schumer (talk | contribs)

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Talk:Schumer lab‎ (diff | hist) . . (+29)‎ . . Schumer (talk | contribs) (Created page with "==Suggested sections to add==")

22 March 2019

15:07

Schumer lab: Commonly used scripts‎ (diff | hist) . . (+356)‎ . . Schumer (talk | contribs) (→‎Scripts that manipulate or summarize fasta files)

			15:01		Schumer lab: Lab group on Sherlock‎‎ (2 changes | history) . . (+448)‎ . . [Schumer‎ (2×)]
					15:01 (cur | prev) . . (+602)‎ . . Schumer (talk | contribs) (→‎Common programs/dependencies and how to load them)
					14:56 (cur | prev) . . (-154)‎ . . Schumer (talk | contribs) (→‎Where to find specific files or programs)

21 March 2019

09:10

BIOL388/S19‎ (diff | hist) . . (-28)‎ . . Kam D. Dahlquist (talk | contribs) (→‎Upcoming Seminars: add oral session for Saturday)

20 March 2019

23:54

(Upload log) . . Desireegonzalez (talk | contribs) uploaded File:BIOL 388 presentation hap4 DG.pdf ‎(presentation)

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