Ucsbgalaxy - User contributions [en]

Bioluminescence Presentations

2014-01-11T16:15:12Z

Oakley:

2014 SICB presentation by Oakley [https://www.dropbox.com/s/fdknl6aezkdrm5d/THO_BioluminescenceSICB2014.pdf]

Bioluminescence Presentations

2014-01-11T16:13:33Z

Oakley:

[https://www.dropbox.com/s/fdknl6aezkdrm5d/THO_BioluminescenceSICB2014.pdf]

Bioluminescence Presentations

2014-01-11T16:12:51Z

Oakley:

<embed_document>https://www.dropbox.com/s/fdknl6aezkdrm5d/THO_BioluminescenceSICB2014.pdf</embed_document>

Bioluminescence Presentations

2014-01-11T16:11:59Z

Oakley: Created page with "<embed_document>http://osiris.eemb.ucsb.edu/IlluminaData/wikifiles/THO_SICB2014.pdf</embed_document>"

<embed_document>http://osiris.eemb.ucsb.edu/IlluminaData/wikifiles/THO_SICB2014.pdf</embed_document>

Lab Publications

2014-01-11T16:10:19Z

Oakley:

*[[Publication Library]]
*[[Lab Papers]]
*[[Lab Theses]]
*[[Lab Presentations]]

Convergent bioluminescence

2014-01-11T16:08:41Z

Oakley:

* [[Vargula tsujii]]
* [[Porichthys notatus]]
* [[Skogsbergia lerneri]]
* [[Sources for luciferin (vargulin)]]

* [[Luciferase Assay]]

* [[Cypridinidae Phylogeny]]
* [[Bioluminescence Presentations]]

Convergent bioluminescence

2014-01-11T16:08:24Z

Oakley:

Cypridinidae Phylogeny

2013-09-25T17:44:13Z

Oakley:

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[http://mbe.oxfordjournals.org/content/30/1/215/F1.expansion.html]]
** OET13 included Regier (2010) data in S. lerneri
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]]

===GenBank Data===
* 18S
** Mainly from Oakley and Cunningham (2002) [[http://labs.eemb.ucsb.edu/oakley/todd/publications/72]]
** Also Yamaguchi and Endo, but this only has V. hilgendorfii, which is also in O&C02 [[http://link.springer.com/article/10.1007/s00227-003-1062-3]]
*16S
** Wakayama see table 1 [[http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2006.00589.x/full#t1]]

==TO DO==
* In MorphoBank, Create separate partitions for binary and multi
* Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

Cypridinidae Phylogeny

2013-09-25T17:36:51Z

Oakley:

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions
* TO DO: Create separate partitions for binary and multi

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[http://mbe.oxfordjournals.org/content/30/1/215/F1.expansion.html]]
** OET13 included Regier (2010) data in S. lerneri
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]]

===GenBank Data===
* 18S
** Mainly from Oakley and Cunningham (2002) [[http://labs.eemb.ucsb.edu/oakley/todd/publications/72]]
** Also Yamaguchi and Endo, but this only has V. hilgendorfii, which is also in O&C02 [[http://link.springer.com/article/10.1007/s00227-003-1062-3]]
*16S
** Wakayama see table 1 [[http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2006.00589.x/full#t1]]

==TO DO==
* Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

Cypridinidae Phylogeny

2013-09-25T17:36:08Z

Oakley:

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions
* TO DO: Create separate partitions for binary and multi

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[http://mbe.oxfordjournals.org/content/30/1/215/F1.expansion.html]]
** OET13 included Regier (2010) data in S. lerneri
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]]

===GenBank Data===
* 18S
** Mainly from Oakley and Cunningham (2002) [[http://labs.eemb.ucsb.edu/oakley/todd/publications/72]]
** Also Yamaguchi and Endo, but this only has V. hilgendorfii, which is also in O&C02 [[http://link.springer.com/article/10.1007/s00227-003-1062-3]]
*16S
** Wakayama see table 1 [[http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2006.00589.x/full#t1]]

===TO DO===
* Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

Cypridinidae Phylogeny

2013-09-25T17:27:03Z

Oakley: /* Transcriptome Data */

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions
* TO DO: Create separate partitions for binary and multi

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[http://mbe.oxfordjournals.org/content/30/1/215/F1.expansion.html]]
** OET13 included Regier (2010) data in S. lerneri
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]]

Cypridinidae Phylogeny

2013-09-25T17:26:37Z

Oakley: /* Transcriptome Data */

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions
* TO DO: Create separate partitions for binary and multi

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii
** OET13 included Regier (2010) data in S. lerneri
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]]

Cypridinidae Phylogeny

2013-09-25T17:24:42Z

Oakley: /* Data Sources */

==Data Sources==
===Morphological matrix===
* Cohen and Morin (2003)
* Uploaded to MorphoBank
* Requires conversion of species names to match other data
** Partly done, but needed for some data partitions
* TO DO: Create separate partitions for binary and multi

===Lisa Torres Matrix===
* Thesis of Vanessa Gonzalez
* 16S, COI, 12S and H3 genes

===Transcriptome Data===
* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii
** OET13 included Regier (2010) data in S. lerneri

Cypridinidae Phylogeny

2013-09-25T17:14:46Z

Oakley:

=Data Sources=

Lab Theses

2013-09-25T17:12:28Z

Oakley:

pdfs now available on lab website:
[[http://labs.eemb.ucsb.edu/oakley/todd/publications]]
Search type=thesis

==PhD Theses==

[[David Plachetzki]]

==MS Theses==
Proposals
{|border="1" cellpadding="5"
|-
! scope="col" | Author and Year
|-
|[[Wilson Thesis Proposal 2006]] MS Thesis
|-
|}

Theses
{|border="1" cellpadding="5"
|-
! scope="col" | Author and Year
|-
|[[Chunghau Lee]]
|-
|[[Bjorn Ostman]]
|-
|[[Asa Wilson]]
|-
|[[Rebecca Lampe 2011]]
|-
|[[Katia Jindrich 2011]]
|-
|}

Lab Theses

2013-09-25T17:09:50Z

Oakley:

pdfs now available on lab website:
[[https://labs.eemb.ucsb.edu/oakley/todd/publications?s=type&o=asc&f[search]=thesis]]

==PhD Theses==

[[David Plachetzki]]

==MS Theses==
Proposals
{|border="1" cellpadding="5"
|-
! scope="col" | Author and Year
|-
|[[Wilson Thesis Proposal 2006]] MS Thesis
|-
|}

Theses
{|border="1" cellpadding="5"
|-
! scope="col" | Author and Year
|-
|[[Chunghau Lee]]
|-
|[[Bjorn Ostman]]
|-
|[[Asa Wilson]]
|-
|[[Rebecca Lampe 2011]]
|-
|[[Katia Jindrich 2011]]
|-
|}

Katia Jindrich 2011

2013-09-25T17:00:15Z

Oakley:

<embed_document>http://osiris.eemb.ucsb.edu/IlluminaData/wikifiles/Thesis_KatiaJINDRICH.pdf</embed_document>

Ostracod Taxonomy

2013-09-20T18:53:14Z

Oakley: Created page with "=Ostracoda= ==Myodocopa== ===Philomedidae=== ====Pseudophilomedinae==== =====Genera===== From Kornicker 1981 #340 "With the addition of the new genus Angulorostrum proposed …"

=Ostracoda=
==Myodocopa==

===Philomedidae===
====Pseudophilomedinae====
=====Genera=====
From [[Kornicker 1981 #340]] "With the addition of the new genus Angulorostrum proposed herein, the Pseudophilomedinae is comprised of 5 genera.
#Angulorostrum Kornicker, 1981 -- [[Kornicker 1981 #340]] reported from 210-1007 m off Brazil, NC, SC, Portugal, Spain.
#Pseudophilomedes Miiller, 1893
#Paramekodon Brady and Norman, 1896
#Tetragonodon Brady and Norman, 1896 - [[Kornicker 1999 #602]] reported depths of 636-2995 m in E Atlantic, Gulf of Mexico, Indian Ocean. Possible empty valves from Puerto Rico and Panama 7-152 m.
#Harbansus Kornicker, 1978

====Philomedinae====
=====Genera=====
Phylogeny in [[Kornicker 1978 #260]] lists 6 genera
# Philomedes
# Igene
# Paraphilomedes
# Euphilomedes
# Scleroconcha
# Anarthron

===Sarsiellidae===
====Dantyinae====
=====Genera=====
Key in [[Kornicker, 1986a: 20]] lists 2 genera
#Dantya
#Nealella
====Sarsiellinae====
=====Genera=====
Key in [[Kornicker, 1986a: 27]] lists 12 genera
#Parasarsiella
#Adelta
#Eusarsiella
#Sarsiella
#Junctichela
#Anscottiella
#Cymbicopia
#Eurypylus
#Ancohenia
#Chelicopia
#Spinacopia
#Neomuelleriella

==Cylindroleberididae==
===Asteropteroninae===
===Cyclasteropinae===
===Cylindroleberidinae===
====Genera====
Key in [[Kornicker, 1986b: 19]] lists 8 genera
#Bruuniella
#Bathyleberis
#Prionotoleberis
#Synasterope
#Heptonema
#Diasterope
#Postasterope
#Parasterope

=Important References=
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/SarsielloidGrantRe.pdf Funded NSF Grant]
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/Kornicker_1984_Philomedid_Gulf.pdf Kornicker 1984-Gulf Philomedidae]
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/Kornicker_Sarsiellid_GulfMex.pdf Kornicker - Gulf Sarsiellidae]

Permits

2013-09-20T18:49:38Z

Oakley:

*[http://osiris.eemb.ucsb.edu/IlluminaData/wikifiles/FKNMS-2009-088_Oakley.pdf FKNMS 2009 Permit]

*Florida Fish and Wildlife Conservation Commission
http://myfwc.com/media/290200/SAL_ScientificResearch.pdf
*National Marine Sanctuary Permits
http://sanctuaries.noaa.gov/management/permits/welcome.html
*Everglades National Park Permits
https://science.nature.nps.gov/research/ac/ResearchIndex
* Spear Fishing Information
http://www.flkeys-diving.com/spearfishing.html

Permits

2013-09-20T18:49:25Z

Oakley:

*[http://osiris.lifesci.ucsb.edu/IlluminaData/wikifiles/FKNMS-2009-088_Oakley.pdf FKNMS 2009 Permit]

*Florida Fish and Wildlife Conservation Commission
http://myfwc.com/media/290200/SAL_ScientificResearch.pdf
*National Marine Sanctuary Permits
http://sanctuaries.noaa.gov/management/permits/welcome.html
*Everglades National Park Permits
https://science.nature.nps.gov/research/ac/ResearchIndex
* Spear Fishing Information
http://www.flkeys-diving.com/spearfishing.html

Main Page

2013-09-20T18:46:40Z

Oakley:

'''Welcome to UCSB's Oakley Lab and Galaxy Wiki'''

* [[UCSB Galaxy Documentation]]

* [[Lab Projects]]
* [[Protocols]]
* [[Career Development]]
* [[Lab Publications]]
* [[Lab Inventory]]
* [[Sequence Run Inventory]]
* [[Ostracod Taxonomy]]

* [[Florida Keys Trip]]

Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [[Wiki Tips]]

== Getting started with Media Wiki==
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Collection Priorities

2012-08-06T04:04:56Z

Oakley:

=Top Priorities=
==Sarsielloidea for Dimorphism Evolution Grant==

===Philomedidae===
====Pseudophilomedinae====
=====Genera=====
From [[Kornicker 1981 #340]] "With the addition of the new genus Angulorostrum proposed herein, the Pseudophilomedinae is comprised of 5 genera.
#Angulorostrum Kornicker, 1981 -- [[Kornicker 1981 #340]] reported from 210-1007 m off Brazil, NC, SC, Portugal, Spain.
#Pseudophilomedes Miiller, 1893
#Paramekodon Brady and Norman, 1896
#Tetragonodon Brady and Norman, 1896 - [[Kornicker 1999 #602]] reported depths of 636-2995 m in E Atlantic, Gulf of Mexico, Indian Ocean. Possible empty valves from Puerto Rico and Panama 7-152 m.
#Harbansus Kornicker, 1978

=====Florida Targets=====
# 100-Compund Eyes of [[Target species Harbansus paucichelatus]]
# 50-Median Eyes of [[Target species Harbansus paucichelatus]]
# 25 Brooding Females of [[Target species Harbansus paucichelatus]]
# [[Target species Pseudophilomedes ferulanus]]
# [[Target species Pseudophilomedes zeta]]
# [[Target species Pseudophilomedes polyancistrus]]
# [[Target species Pseudophilomedes ambon]]

====Philomedinae====
=====Genera=====
Phylogeny in [[Kornicker 1978 #260]] lists 6 genera
# Philomedes
# Igene
# Paraphilomedes
# Euphilomedes
# Scleroconcha
# Anarthron

===Sarsiellidae===
====Dantyinae====
=====Genera=====
Key in [[Kornicker, 1986a: 20]] lists 2 genera
#Dantya
#Nealella
====Sarsiellinae====
=====Genera=====
Key in [[Kornicker, 1986a: 27]] lists 12 genera
#Parasarsiella
#Adelta
#Eusarsiella
#Sarsiella
#Junctichela
#Anscottiella
#Cymbicopia
#Eurypylus
#Ancohenia
#Chelicopia
#Spinacopia
#Neomuelleriella

=====Florida Targets=====
# [[Target species Eusarsiella zostericola]]
# [[Target species Eusarsiella spinosa]]
# [[Target species Eusarsiella texana]]
# [[Target species Eusarsiella ozotothrix]]
# [[Target species Eusarsiella disparalis]]
# [[Target species Dantya heardi]]
# [[Target species Parasterope muelleri]]
# [[Target species Postasterope messingi]]
# [[Target species Parasterope pollex]]
# [[Target species Asteropella maclaughlinae]]
# [[Target species Actinoseta chelisparsa]]
# [[Target species Amboleberis americana]]
# [[Target species Asteropterygion oculitristis]]
# [[Target species Actinoseta hummelincki]]
#
#
#
#
#
#
#
#

=Secondary Priorities=
==Luciferase Project -- Lead is Nicole Leung==
# [[Target species Skogsbergia lerneri]] - Preserve for RT-PCR of luciferase homologs
# Any luminescent species - Preserve for Next-Gen
# [[Target species Skogsbergia lerneri]] - Preserve for in situ hybridization

==Podocopa for ATOL project==
# [[Target Family - Cytherettidae]]

==Cylindroleberididae==
===Asteropteroninae===
===Cyclasteropinae===
===Cylindroleberidinae===
====Genera====
Key in [[Kornicker, 1986b: 19]] lists 8 genera
#Bruuniella
#Bathyleberis
#Prionotoleberis
#Synasterope
#Heptonema
#Diasterope
#Postasterope
#Parasterope

=Important References=
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/SarsielloidGrantRe.pdf Funded NSF Grant]
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/Kornicker_1984_Philomedid_Gulf.pdf Kornicker 1984-Gulf Philomedidae]
* [http://macroevolution.lifesci.ucsb.edu/IlluminaData/wikifiles/Kornicker_Sarsiellid_GulfMex.pdf Kornicker - Gulf Sarsiellidae]

Day by Day

2012-07-28T12:44:14Z

Oakley: /* Oakley Family */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 8=
1. Morning - finish sorting and preserving Ft. Pierce samples

==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 2.5 hours drive from Ft. Pierce to MIA
# Leave by 4 to meet other Other Lab Crew

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00am 4718 Calle Reina
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM
==Drive to KML==
*Approx 2.5 hrs from MIA

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T12:42:42Z

Oakley: /* August 8 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 8=
1. Morning - finish sorting and preserving Ft. Pierce samples

==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 2.5 hours drive from Ft. Pierce to MIA
# Leave by 4 to meet other Other Lab Crew

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00am 4718 Calle Reina
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T12:41:20Z

Oakley: /* August 7 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 2.5 hours drive from Ft. Pierce to MIA
# Leave by 4 to meet other Other Lab Crew

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00am 4718 Calle Reina
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T12:39:40Z

Oakley: /* Crew 1 Drive from Ft. Pierce through Miami to Keys */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 2.5 hours drive from Ft. Pierce to MIA
# Leave by 4 to meet other Other Lab Crew

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00am 4718 Calle Reina
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T12:32:38Z

Oakley: /* Oakley Family */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00am 4718 Calle Reina
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T12:05:49Z

Oakley: /* Saturday August 4 - Todd fly to Ft. Lauderdale */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 =

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:35:34Z

Oakley: /* Monday Aug 6 - Day 3 - Fort Pierce, FL */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Todd fly to Ft. Lauderdale=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Sampling with small boat at Smithosonian Marine Lab in Ft. Pierce

=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:34:33Z

Oakley: /* Saturday August 4 - Day 1 - not everyone has to arrive on Day 1 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Todd fly to Ft. Lauderdale=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:33:58Z

Oakley: /* Crew 1 Drive from Ft. Pierce to Miami */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce through Miami to Keys==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:32:53Z

Oakley: /* Lab */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
*Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
*Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:32:17Z

Oakley: /* Crew 1 Drive from Ft. Pierce to Miami */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

==Crew 2 Fly to Miami==
===Lab===
Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:32:02Z

Oakley: /* August 7 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Lab===
Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:30:53Z

Oakley: /* Sunday Aug 5 - Day 2 - Fort Pierce, FL */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Fly into Miami
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Lab===
Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:30:09Z

Oakley: /* Saturday August 4 - Day 1 - not everyone has to arrive on Day 1 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Lab===
Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:10:17Z

Oakley: /* Crew 2 Fly to Miami */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=
# Fly into Miami Nicole
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Lab===
Marko LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Bryan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM
Dan LAX 08 AUG 12 700AM MIA 08 AUG 12 715PM

===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:06:05Z

Oakley: /* Oakley Family */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=
# Fly into Miami Nicole
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Oakley Family===
*RoadRunner Shuttle to arrive LAX at 8:00
**Reservation number 932768
*Flight
**Record Locator:NDFQTT
**LAX -> ORD 9:30 AM Arrives: 3:30 PM
**ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T11:05:37Z

Oakley: /* Crew 2 Fly to Miami */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=
# Fly into Miami Nicole
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==
===Oakley Family===
-RoadRunner Shuttle to arrive LAX at 8:00
--Reservation number 932768
-Flight
--Record Locator:NDFQTT
--LAX -> ORD 9:30 AM Arrives: 3:30 PM
--ORD -> MIA 4:15 PM Arrives: 8:20 PM

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T10:58:08Z

Oakley: /* Saturday August 4 - Day 1 - not everyone has to arrive on Day 1 */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=
# Fly into Miami Nicole
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
##Emily BOS 05 AUG 12 1130AM MIA 05 AUG 12 250PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Day by Day

2012-07-28T10:56:45Z

Oakley: /* Day 5 - Keys Marine Lab, Layton, FL */

The schedule will evolve here, starting with a sketch, ultimately ending with a detailed plan.
=Thursday Aug 2 - Pre-collecting -- Todd at Whitney Marine Lab=
# Todd Flies to Orlando -- SBA 02 AUG 12 605AM --> MCO 02 AUG 12 425PM

=Friday August 3 - Pre-collecting -- Todd at Whitney Marine Lab=
# 11:00 Todd gives departmental seminar at Whitney Lab
= Saturday August 4 - Day 1 - not everyone has to arrive on Day 1=
# Fly into Miami Nicole
##Nicole LAX 05 AUG 12 900AM MIA 05 AUG 12 525PM
##Celia DTW 05 AUG 12 830AM MIA 05 AUG 12 518PM
# Rent van
# Stay at Local Hotel Near Smithsonian Marine Lab, Fort Pierce

= Sunday Aug 5 - Day 2 - Fort Pierce, FL=
# Sample in Indian River, use small boat from Smithsonian
# Sort all samples, can use Smithsonian Labs with dissecting scopes
= Monday Aug 6 - Day 3 - Fort Pierce, FL=
# Additional Samping near Ft Pierce?
# Oakley to visit Whitney Marine Lab for talk? However, this is 3 hours' drive one way from Ft. Pierce
=August 7=
# About 6-7 hours drive from Ft. Pierce to Layton
# Will go through Miami and can pick up people at airport
# Stay at Keys Marine Lab

=August 8=
==Crew 1 Drive from Ft. Pierce to Miami==
==Crew 2 Fly to Miami==

=Day 6 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 7 - Keys Marine Lab, Layton, FL=
# Sampling near KML
=Day 8 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 9 - Keys Marine Lab, Layton, FL=
#Sampling near KML
=Day 10 - Keys Marine Lab, Layton, FL=
#Sampling near KML
#Drive to Mote

=Day 11 - Mote Tropical Research Station=
#Sampling near Mote
=Day 12 - Mote Tropical Research Station=
#Sampling near Mote
=Day 13 - Mote Tropical Research Station=
#Sampling near Mote
=Day 14 - Fly Home=

Pancrustacean MegaTree

2012-07-03T11:25:16Z

Oakley: /* Amino Acid Data */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked here [* The amino acid data are here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-amino-acid-data]].
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* The amino acid data are here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-amino-acid-data]
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file: mtGenome.tab .
* For no apparent reason, a few amino acid sequences did not download, despite the fact that NT sequences and in at least some cases, translations, are available. These perhaps should be added manually. Also it seems some charonda sequences are duplicated in the AA file, perhaps because there are sub-species. The list of missing AA sequences is here:

Sasakia_charonda ATP6
Sasakia_charonda ATP8
Sasakia_charonda COI
Sasakia_charonda COII
Sasakia_charonda COIII
Sasakia_charonda CYTB
Hipparchia_autonoe CYTB
Anopheles_funestus ATP6
Anopheles_funestus ATP8
Anopheles_funestus COIII
Anopheles_funestus ND2
Anopheles_funestus ND4
Anopheles_funestus ND4L
Agriosphodrus_dohrni COI
Agriosphodrus_dohrni COII
Agriosphodrus_dohrni COIII

====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are a few such genes, listed above.

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T11:24:43Z

Oakley: /* Amino Acids */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* The amino acid data are here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-amino-acid-data]
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file: mtGenome.tab .
* For no apparent reason, a few amino acid sequences did not download, despite the fact that NT sequences and in at least some cases, translations, are available. These perhaps should be added manually. Also it seems some charonda sequences are duplicated in the AA file, perhaps because there are sub-species. The list of missing AA sequences is here:

Sasakia_charonda ATP6
Sasakia_charonda ATP8
Sasakia_charonda COI
Sasakia_charonda COII
Sasakia_charonda COIII
Sasakia_charonda CYTB
Hipparchia_autonoe CYTB
Anopheles_funestus ATP6
Anopheles_funestus ATP8
Anopheles_funestus COIII
Anopheles_funestus ND2
Anopheles_funestus ND4
Anopheles_funestus ND4L
Agriosphodrus_dohrni COI
Agriosphodrus_dohrni COII
Agriosphodrus_dohrni COIII

====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are a few such genes, listed above.

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T11:11:27Z

Oakley: /* Amino Acids */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file: mtGenome.tab .
* For no apparent reason, a few amino acid sequences did not download, despite the fact that NT sequences and in at least some cases, translations, are available. These perhaps should be added manually. Also it seems some charonda sequences are duplicated in the AA file, perhaps because there are sub-species. The list of missing AA sequences is here:

Sasakia_charonda ATP6
Sasakia_charonda ATP8
Sasakia_charonda COI
Sasakia_charonda COII
Sasakia_charonda COIII
Sasakia_charonda CYTB
Hipparchia_autonoe CYTB
Anopheles_funestus ATP6
Anopheles_funestus ATP8
Anopheles_funestus COIII
Anopheles_funestus ND2
Anopheles_funestus ND4
Anopheles_funestus ND4L
Agriosphodrus_dohrni COI
Agriosphodrus_dohrni COII
Agriosphodrus_dohrni COIII

====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are a few such genes, listed above.

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T11:02:03Z

Oakley: /* Nucleotide Data */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file: mtGenome.tab .
* For no apparent reason, a few amino acid sequences did not download, despite the fact that NT sequences and in at least some cases, translations, are available. These perhaps should be added manually. The list is here:

Sasakia_charonda ATP6
Sasakia_charonda ATP8
Sasakia_charonda COI
Sasakia_charonda COII
Sasakia_charonda COIII
Sasakia_charonda CYTB
Hipparchia_autonoe CYTB
Anopheles_funestus ATP6
Anopheles_funestus ATP8
Anopheles_funestus COIII
Anopheles_funestus ND2
Anopheles_funestus ND4
Anopheles_funestus ND4L
Agriosphodrus_dohrni COI
Agriosphodrus_dohrni COII
Agriosphodrus_dohrni COIII

====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are a few such genes, listed above.

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T11:00:51Z

Oakley: /* Amino Acids */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file: mtGenome.tab .
* For no apparent reason, a few amino acid sequences did not download, despite the fact that NT sequences and in at least some cases, translations, are available. These perhaps should be added manually. The list is here:

Sasakia_charonda ATP6
Sasakia_charonda ATP8
Sasakia_charonda COI
Sasakia_charonda COII
Sasakia_charonda COIII
Sasakia_charonda CYTB
Hipparchia_autonoe CYTB
Anopheles_funestus ATP6
Anopheles_funestus ATP8
Anopheles_funestus COIII
Anopheles_funestus ND2
Anopheles_funestus ND4
Anopheles_funestus ND4L
Agriosphodrus_dohrni COI
Agriosphodrus_dohrni COII
Agriosphodrus_dohrni COIII

====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are 300+ such genes. Many of these were probably already present in the 6-gene dataset, such that Seth deleted those manually from the AA. '''These discrepancies must be solved.'''

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T09:29:16Z

Oakley: /* Data Sets */

=Introduction=
=Methods=
==Data Sets==
===EST===
===New 454===
===Full Genomes===
===Regier 62-gene protein coding===
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file
mtGenome.tab
====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are 300+ such genes. Many of these were probably already present in the 6-gene dataset, such that Seth deleted those manually from the AA. '''These discrepancies must be solved.'''

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T09:15:30Z

Oakley: /* Mitochondrial Genomes */

=Introduction=
=Methods=
==Data Sets==
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
====Amino Acids====
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file
mtGenome.tab
====Nucleotide Data====
* For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are 300+ such genes. Many of these were probably already present in the 6-gene dataset, such that Seth deleted those manually from the AA. '''These discrepancies must be solved.'''

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T09:13:26Z

Oakley: /* Amino Acid Data */

=Introduction=
=Methods=
==Data Sets==
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
**''' Seth is working on the CO1 AA data.'''

===Mitochondrial Genomes===
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file
mtGenome.tab

* That is the proteome data. For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are 300+ such genes. Many of these were probably already present in the 6-gene dataset, such that Seth deleted those manually from the AA. These discrepancies must be solved.

=Results=
=Discussion=

Pancrustacean MegaTree

2012-07-03T09:13:04Z

Oakley: /* Mitochondrial Genomes */

=Introduction=
=Methods=
==Data Sets==
===6-gene Data Set===
* Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus
is duplicated with 12S being in both 6-genes, and in mtRNAgenomes. Seth then wrote "There was a typo in the file. That is why I didn't delete the duplicate Pollicipes_polymerus 12S between the two files, Pollicipes_polymerus 16S will also be duplicated. So, you are going to have to cut that out of the six gene data set. "
* After uploading to Galaxy, THO used find and replace to replace sp. with sp The reason for this is that the "." after sp can sometimes be problematic in some programs. To standardize species names, we should try to always leave off the period after the sp.
* THO uploaded the 6-gene NT data set to Galaxy, and it can be found on the kGalaxy history linked here [ http://knot.cnsi.ucsb.edu:8080/u/ostratodd/h/pancrustacea-megatree-data]
* That kGalaxy history has a MUSCLE alignment, and phylocatenator grid to view presence/absence of each gene.
====Amino Acid Data====
* The 6-gene dataset was first compiled as DNA. However, our other datasets are mainly analyzed as amino acids. As such, we need the translated data for CO1 and Histone. The other genes are rDNA.
** In an email dated June 29, Seth sent the translated H3 sequences in a file. THO uploaded to the Galaxy history linked above.
** Seth is working on the CO1 AA data.

===Mitochondrial Genomes===
* Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
* The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
* The accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list.
* In addition, Alignments for each gene can be downloaded by clicking on links toward the top of the page. These are saved in individual fasta files named by gene as *.fa in the directory above. THO then converted to tabular format using the shell script 1_make_tables, which calls the perl script getSpeciesofGB.pl for each gene. That perl script pulls out the species name of each accession from GenBank, and writes a tabular file, which is concatenated together into the file
mtGenome.tab

* That is the proteome data. For the rDNA data, THO wrote scripts to parse data from GenBank files. These are in the subdirectory gbstrip of the directory listed above.
* The next step is to use BioPerl to download all the GenBank files directly from GenBank, using the list of genome accession numbers explained above. This is done using the script getGB.pl. The actual command is:
./getGB.pl AccList.tx > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
* The next step is to use genbankstrip.pl, a script written by Olaf Bininda-Emonds. The script pulls genes from a genbank file based on name. Many genes, especially mt genes have many different synonyms. These can be added into the script such that all synonyms are pulled out into one file. All the synonyms for 12S and 16S collapse into mtrnr1 and mtrnr2.
* All the other genes collapse into a single file as well. However, some synonyms might not be completely accounted for. Final tallies for each gene are listed in the file synonyms_list.dat
* All the files can be rebuilt by simply calling the shell script named: 1_pull_nucs . This calls genbankstrip.pl for each gene and calls a custom perl script to get additional data for phytab format, including species name and genbank id.
* THO uploaded the NT dataset for mt coding genes to the history above. THO subtracted datasets to find genes present as NT but not as AA. There are 300+ such genes. Many of these were probably already present in the 6-gene dataset, such that Seth deleted those manually from the AA. These discrepancies must be solved.

=Results=
=Discussion=