Current To Do List Portal 9-3-13

2015-06-07

++ Current To Do List Portal 9-3-13

Current To Do List
[Some Finished To Do List Items portal 9-3-13]

[Recent Places portal 9-3-13]

[Event Based To Do List portal 9-3-13]

[Hopeful To Do List 2-28-12]

[Long term to do list 6-12-14]

[Cleaning and organizing stuff 07-13-2014d1003]

-take care of notebook notes 06-07-2015d1223
--E:\temp\notebook notes (home computer)

-quantitate colonies for colony formation assay 06-07-2015d1111
--http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/colony%20formation%20assay
--[cni_keratinocyte colony formation assay 5-30-15]

-organize histopathology slide data 06-07-2015d0911
--http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/Histopathology%20slide%20receipts
--photos of histopathology slide boxes and labels
---http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/photos%20of%20histopathology%20slide%20boxes%20and%20labels

analyze pathology results; 05-27-2015d2353
{
from:	Juana María Flores <jflores@vet.ucm.es>
to:	"Whittemore.Kurt" <kwhittemore@cnio.es>
date:	Wed, May 27, 2015 at 7:30 PM
subject:	histopath 5-5-15
}

-attend to sphider-plus email
--
{
from:	Dipl.-Ing. Rolf Kellner <tec@sphider-plus.eu>
to:	Kurt Whittemore <kurtwhittemore@gmail.com>
date:	Wed, May 20, 2015 at 12:02 AM
subject:	Sphider-plus
}

-deal with Juan Molina's email
--
{
from:	Molina.Juan_Ramón <jrmolina@cnio.es>
to:	"Whittemore.Kurt" <kwhittemore@cnio.es>
date:	Tue, May 19, 2015 at 11:43 AM
subject:	RE: planning for student visa
}

-attend to neurodegeneration CBA 
--
{
from:	Secretaria Ceiyba <secretariaceiyba@isciii.es>
to:	"Whittemore.Kurt" <kwhittemore@cnio.es>
cc:	"Ramos.Celia_Maria" <cmramos@srv.cnio.es>,
"Blanco.Isabel" <iblanco@srv.cnio.es>
date:	Wed, May 13, 2015 at 9:36 AM
subject:	Remisión observaciones CBA 23_2015
}
--neurodegeneration CBA revision deadline is June 12th
--need to get translation from Susa 06-07-2015d1653

-analyze HT Q-FISH data 05-22-2015d1430
--located here (temporarily): C:\temp_sync\HT Q-FISH results 05-22-2015d1152\Nuclei
--see also [cni_Q-FISH for 3rd round of TRF1 blood samples 03-30-2015d1220]

measure amyloid beta in brain of tert ko mice; 05-04-2015d1419

request confocal microscope training

-buy tripod for camera; SANYO and the model HD XACTI (7.1 megapixel); 05-04-2015d1830

make a list of software and projects to contribute to regularly

-need to find papers studying neurogenesis in the brain

setup user accounts in Pydio

-look through CNIO scientific report; email "the 2014 Scientific Report is now online" 3-26-15 from scerda@cnio.es;  04-03-2015d1127

-look at DNA damage in TRF1 (maybe you can even do it genome-wide?)
--email 1-30-15 subject "copy of presentation"; https://mail.google.com/mail/u/0/#search/copy+of+presentation/14b364c39749e008

-maybe try some toxic treatments known to induce parkinson or alzheimer and see whether the TERT KO are more susceptible
--email 1-30-15 subject "copy of presentation"; https://mail.google.com/mail/u/0/#search/copy+of+presentation/14b364c39749e008

-do regular Q-FISH on 1 yo and 2 yo TRF1 mice for skin brain and intestine tissues (Elisa and I already did heart)

-sort eGFP-TRF1 hi and lo cells from intestine and skin and perform gene expression analysis to see whether they are like stem cells
--need to prepare for this protocol
-induce cancer in some TRF1 mice and controls with DMPA/TPA

-analyze Christian's heart infarct data using the cardiac regeneration specific geneset from the heatmap (or something) in the paper titled "Complete cardiac regeneration in a mouse model of myocardial infarction"
--[cni_heart infarct gene expression experiment 12-04-2014d1931]

-longterm: read Ralph Schneider's dissertation

-take a look at papers from Bioinformatics group 11-17-2014d1531
--"C:\Sync\cnio\2014\2014\11-17-2014d1104\papers from Bioinformatics group 11-17-2014d1529"
--[Emerging methods in protein co-evolution]

-look at Overview of Mouse Models of Parkinson's Disease paper; ch 06-07-2015d1658
-take a look at Correction of Pathological Accumulation of Glycosaminoglycans in Central Nervous System and Peripheral Tissues of MPSIIIA Mice Through Systemic AAV9 Gene Transfer paper

-take a look at paper from Diego
--Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer

-maybe compare human, mouse, and cow telomerase with bowhead whale telomerase (maybe look at shelterin proteins as well)

-possibly gradually go through TRF1 sequence from ocr and make sure that everything is corrected

-review information related to how I can do my postdoc projects
--continually review all the things to keep track of the different projects
--make plans for upcoming tasks
-learn Spanish
-learn bioinformatics
-work on complex adaptive system metric project (aka characterizing networks with age project)

------------------------
See also
-[Code I may want to write]

---------------------------
Some finished to do list items (some items)
-analyze new pet data; ch 05-26-2015d2311
--email about this here
---
{
from:	Cámara.Juan_Antonio <jacamara@cnio.es>
to:	"Whittemore.Kurt" <kwhittemore@cnio.es>
date:	Mon, May 18, 2015 at 2:59 PM
subject:	
}
-make sure to remove large files from here; 05-11-2015d1128; ch 05-26-2015d2313
E:\kurt\storage\projects\cnio\lgdata_DR\2015\05 May\05-08-2015d1358\object recognitin 8-5-15
-analyze TRF1 immunofluorescence data; ch 05-25-2015d2228
-perform HT Q-FISH on collected mouse TRF1 samples; 05-06-2015d1116; ch 05-25-2015d2229
 -update Fulbright profile; ch 05-25-2015d2229
 --see
 {
 from:	Tory Leech <tleech@comision-fulbright.org>
to:	
cc:	Victoria Ruiz <vruiz@comision-fulbright.org>
bcc:	kurtwhittemore@gmail.com
date:	Tue, Apr 21, 2015 at 9:42 AM
 }
-add something about detecting respiratory symptoms in mice to lung cancer cba.; 05-11-2015d1041; ch 05-21-2015d2048
--e.g. resistance of lung or elasticity of lung.  Juanma said he knew someone that knew the name of the machine that can quantitate these things
-do Spain taxes; ch 05-19-2015d2315
--note from Juan Molina about people or organizations that might be able to help me with Spain taxes
---email "help with taxes" 4-6-15 from "	Molina.Juan_Ramón <jrmolina@cnio.es> "
-order materials for colony formation assay; ch 05-19-2015d2316
{
from:	Martinez.Paula <pmartinez@cnio.es>
to:	Kurt Whittemore <kurtwhittemore@gmail.com>,
"Tejera.Agueda" <atejera@cnio.es>
date:	Fri, May 15, 2015 at 10:50 AM
subject:	Re: materials for colony formation assay
}
-a few notes
{
Cian has mitomycin C
Noelia has the media I need
I need to order: plates, fibronectin, calcium chloride (CaCl2) 1 M solution
}
-look into plan to get visa and Fulbright issue; ch 05-14-2015d1418
-figure out how to get Fulbright medical records done; ch 05-14-2015d1423 (I'll do it in Utah)
--reference email "2015-2016 Fulbright U.S. Scholar Grant Selection Status" 2-10-15
-analyze old tail suspension data; ch 05-11-2015d1659
--I was going to go back and reanalyze the old tail suspension videos with the automatic analysis method, but then I realized that those videos did not have the black background so they can't be analyzed.
-deal with yahoomail bioinformatic emails; ch 05-06-2015d1301
-put text from CBBAs into wiki for better searchability; 04-04-2015d1111; ch 05-06-2015d1137
-finish preparing lung cancer CBBA, and refer to email thread with Rosa "mice for lung cancer project" around the time of 3-24-15; 04-03-2015d1122 ; ch 05-06-2015d1140
-look into amazon cloud drive pydio issue; ch 05-06-2015d1140 (I don't think I'll look into this more)
--email subject: "[Pydio, formerly AjaXplorer] Amazon Cloud Drive"
-move the lung cancer aav9-tert; ch 05-06-2015d1141
--need to make a cbba for this
-CBBA animal approval issue; ch 05-06-2015d1142
--need CBBA for lung cancer project; 03-01-2015d1533
analyze object recognition; ch 05-06-2015d1121
-straighten out issue with referenced publications in KRAS CBA; ch 05-05-2015d1732
-fix KRAS CBA issues; ch 05-05-2015d1732
--address comments from Maria Garcia
{
from:	Garcia.Maria <mgarciab@cnio.es>
to:	"Whittemore.Kurt" <kwhittemore@cnio.es>
date:	Tue, Apr 14, 2015 at 9:10 PM
subject:	Re: Kras Lung Cancer CBA
}
--address comments from Rosa
{
anesthesia and analgesic info here
{
from:	Serrano.Rosa <rserrano@cnio.es>
to:	Kurt Whittemore <kurtwhittemore@gmail.com>
date:	Tue, Apr 14, 2015 at 7:17 PM
subject:	Re: anesthesia and analgesic questions
}
}
 -record CBBA process ch 05-05-2015d1437
 --see
 {
 from:	Tejera.Agueda <atejera@cnio.es>
to:	Kurt Whittemore <kurtwhittemore@gmail.com>
date:	Tue, Apr 21, 2015 at 5:15 PM
subject:	Re: stamped documents
 }
-record notes on Definiens; ch 05-04-2015d1830
-try out pdf note extractor app; ch 05-04-2015d1421
-analyze pathology data; ch 05-04-2015d1421
-analyze rotarod, tightrope, and tail suspension tests; ch 05-04-2015d1421
-figure out how to do automatic analysis of tail suspension videos; ch 05-04-2015d1421
-extract annotations from genes proteins and computers book; ch 05-04-2015d1422
--E:\kurt\storage\Documents\Books\2015\4 April\04-20-2015d0900
-look into Spain tax issue; ch 05-04-2015d1422
-finish dealing with Genes proteins and computers book annotatons; 4-5-15; ch 05-04-2015d1423
-analyze pathology results from Juana; ch 05-04-2015d1423
--email "results" 2-16-15 from jflores@vet.ucm.es (wrote notes)
--and email "histopatologia" 3-16-15 from "jflores@vet.ucm.es" (wrote notes)
-continue with iodine video; ch 5-3-15
--https://www.youtube.com/watch?v=ku2lylX13h4
--figure out dose for neurodegeneration CBA; 04-21-2015d2120
--anesthesia and analgesic info here
{
from:	Serrano.Rosa <rserrano@cnio.es>
to:	Kurt Whittemore <kurtwhittemore@gmail.com>
date:	Tue, Apr 14, 2015 at 7:17 PM
subject:	Re: anesthesia and analgesic questions
}
-order more slides for "1" slides; 04-04-2015d1111
-order more gray boxes; 04-21-2015d1500
-setup goodsync, and bittorrent sync
-I think I will repeat the TRF1 embryo immunofluorescence experiment with just 2 slides with two replicates (4 slides total) with different permeabilization times to test the conditions.
-deal with CBBA issue; 04-03-2015d1105
--email "IACUC.018-2015" 4-1-15
-deal with TERT probe issue; 04-03-2015d1105; emailed Paula about it 04-04-2015d2004
--email "question about Terf probes" 4-1-15 (Transnetyx email)
-CBBA animal approval issue
--CBBA for neurodegeneration project; ch pre 04-04-2015d1954
--CBBA for TRF1 mice and include DMBA+TPA treatment; ch pre 04-04-2015d1954
-read Maria Garcia's dissertation; finished pre 04-04-2015d1953
-look at ARCS foundation request; I think too much time has passed to look into this issue 04-04-2015d1951
-continue with "Metropolis Algorithms for Representative Subgraph Sampling" paper; 03-30-2015d2311
-look into testing compounds in blood issue
--https://mail.google.com/mail/u/0/#search/compounds+in+blood/14badca897caa621
-let Gema know she can contact the other guy for the SAMP8 mice; 03-13-2015d1339
--email "SAMP8 mice" 3(mar)-5-15 1:12pm gluque@srv.cnio.es
-Treat TERT KO mice with compound that induces neurodegeneration; 03-13-2015d1340 (well not done, but progress should be made later)
--look at the "Parkinson's Disease Models.pdf" paper from Maria and order the compounds; pre 03-03-2015d1247
-make sure to make record of approximating search information entropy, and clean up the code; 03-08-2015d2317
-Order SAMP8 mice with help from Rosa Serrano; no longer applicable. . 03-03-2015d1249
-maybe get SMC data for Shen; ch 03-01-2015d2233
-CBBA animal approval issue
--CBBA for neurodegeneration project; 03-01-2015d1533
--CBBA for TRF1 mice and include DMBA+TPA treatment; 03-01-2015d1533
-take a look at melatonin article; ch 02-21-2015d2341
--http://www.lef.org/magazine/2007/6/nu_melatonin/Page-01
-send Gema Luque animal certificate when I get it; 02-09-2015d2254; ch pre 02-13-2015d1220
-do more cognitive tests in tert ko mice; ch 02-13-2015d1220 (I determined that I should do these tests around April 7th)
-do gene expression analysis on embryonic fibroblasts; ch 02-13-2015d1221
-get certificate for working with animals from the animalaria; pre 02-13-2015d1222
-look at tail suspension data in light of new weight data; 02-11-2015d1640
--weights acquired around 1-8-14 (email subject "Transnetyx results" 1-8-14 https://mail.google.com/mail/u/0/?tab=wm#search/weights/14a77e98b600d96c)
---"C:\Sync\cnio\2015\01 January\01 January\01-09-2015d1110\weights of some tert ko mice\Weights of some tert ko mice and controls 01-09-2015d1604.pdf"
---weights in spreadsheet
----"C:\Sync\cnio\2015\01 January\01 January\01-09-2015d1110\weights of some tert ko mice\Weights of some tert ko mice and controls in spreadsheet 1-9-15.xlsx"
-do KI67 with Elisa with hearts on eGFP-TRF1 mice; 01-30-2015d1059
--attend to trf1 embryo gene expression data; 01-30-2015d1059
--[cni_microarray experiment for trf1 embryos 01-08-2015d1947]
--C:\Sync\cnio\lgdata_DR\2015\01 January\01-22-2015d1728\trf1 embryo gene expression data\20150122_KWhittemore_ServiceReport
-look into Life Extension Europe; ch 01-25-2015d1325
-analyze tail suspension test videos 12-4-14; 01-25-2015d1109
--[cni_tail suspension test 12-04-2014d1644]; 01-24-2015d1237
and also
--C:\Sync\cnio\lgdata_DR\2014\December\December\12-12-2014d1213\tail suspension test videos
-analyze confocal data found here; 01-25-2015d1106
--[cni_Q-FISH for 2 backup plates 01-14-2015d2142]
-[some finished to do list items pre 01-25-2015d1107]

azim58wiki: