Tuesday, April 26, 2016

QUBEHUB software for simulations

Including RStudio, XPPAUT, PPLane etc.

https://qubeshub.org/resources/software

PLAS power law analysis and simulation

Voit book, software support for ODE analysis

http://enzymology.fc.ul.pt/software/plas/

Atlanta QBIO book orders



Books to order:


A first course in systems biology, By Eberhard Voit
ISBN: 9780815344674, Garland
$135


Physical models of living systems,  by Philip Nelson
ISBN-10: 1-4641-4029-4; ISBN-13: 978-1-4641-4029-7;
$150


Mathematics for the life sciences,  by Erin N. Bodine, Suzanne Lenhart, Louis Gross
ISBN-13: 9780691150727, Publisher: Princeton University Press
$70
A Biologist's Guide to Mathematical Modeling in Ecology and Evolution, by Sarah P. Otto Troy Day , ISBN: 781400840915,  Publisher: Princeton University Press
$80


Mathematical Modeling in Systems Biology: An Introduction, by Brian P Ingalls,
Publisher: The MIT Press; 1 edition (July 5, 2013), ISBN-10: 0262018888, ISBN-13: 978-0262018883
$55

Data Wise, Revised and Expanded Edition: A Step-by-Step Guide to Using Assessment Results to Improve Teaching and Learning

http://www.amazon.com/Data-Revised-Expanded-Step---Step/dp/161250521X/ref=sr_1_4?ie=UTF8&qid=1461701152&sr=8-4&keywords=education+assessment



Discipline-Based Education Research: A Guide for Scientists Paperback – July 16, 2015

http://www.amazon.com/Discipline-Based-Education-Research-Guide-Scientists/dp/1515024563/ref=sr_1_fkmr0_1?ie=UTF8&qid=1461701711&sr=8-1-fkmr0&keywords=Discipline-based+education+research+%E2%80%93+A+guide+for+scientists%2C+2nd+Edition.


References:
http://www.lifescied.org/site/misc/ifora.xhtml


-Schneider B, Carnoy M, Kilpatrick J, Schmidt WH, & Shavelson R. (2007). Estimating causal effects: Using experimental and observational designs. American Educational Research Association: Washington DC.
-Weimer, M. (2006). Enhancing scholarly work on teaching and learning. Jossey-Bass: San Francisco.

(to read) Kaya, Ma, sanger strain lifespan study


 Defining Molecular Basis for Longevity Traits in Natural Yeast Isolates
Alaattin Kaya1,#, Siming Ma1,#, Brian Wasko2, Mitchell Lee2, Matt Kaeberlein2, and Vadim N. Gladyshev1,*
1Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA

RLS were provided

todo: download data, and Sanger resource data


Growth rates were determined using a Bioscreen C MBR machine by analysis of optical density in the OD420-580 range as previously described in combination with the YODA Software package18. The data on transcripts, peptides (proteins), metabolites and morphology were downloaded from Yeast Resource Center http://www.yeastrc.org/g2p/download.do. Values corresponding to the 22 strains were extracted; metabolite data were not available for 378604X. Metabolites with missing values in more than one strain (other than 378604X) were discarded; the remaining missing values (6 out of 107 metabolites) were imputed based on 10 nearest neighbors, using “knnImputation” function of R package “DMwR”. For comparison across the phenotypic data, the values were standardized across the strain by setting mean = 0 and standard deviation = 1. In addition, for genes represented by multiple peptides, we calculated the mean standardized values to perform the regression.



(to read) Yang 2015 PNAS yeast GFP screen, asymmetric partition

GFP library screen, Cy5 labeling of cell wall, daughters have few cy5 because their walls are newly synthesized.

Most proteins are symmetrically distributed.

All aging factors are 'non-essential'.  This means that their 'interactions' to essential genes should be of importance in my network aging model.



Thursday, April 21, 2016

yeast DNA repair genes

Gene Ontology Term: DNA repair


GO ID
GO:0006281
Aspect
Biological Process

http://www.yeastgenome.org/go/GO:0006281/overview

SIR2
protein  NP_010242.1
http://www.ncbi.nlm.nih.gov/protein/6320163?report=fasta

https://www.ncbi.nlm.nih.gov/nucleotide/296143322?report=genbank&log$=nucltop&blast_rank=1&RID=HJD968YR01R






RFA1










desktop flow cytometer survey

Main fluophores: 
  Propidum Iodide (PI), dihydroethydium (DHE), and dihydrorhodamine (DHR)

My understanding of the basic configuration are (based on CALIBUR):
 blue laser 488nm + red laser 635nm (optional)
Detector channels: FSC, SSC, FL1 green 530nm, FL2 yellow 585, FL3 red 670nm, with an optional  FL4 661nm. 


http://qa.ff.up.pt/~quimicafisica/405.pdf

Vendors and models

BioRad S3e Cell Sorter

easyCyte
http://www.emdmillipore.com/US/en/life-science-research/cell-analysis/guava-easycyte-flow-cytometers/zLWb.qB.7eAAAAE_1rFkifKv,nav?cid=BI-XX-BDS-P-GOOG-FLOW-B323-1017

http://www.emdmillipore.com/US/en/life-science-research/cell-analysis/guava-easycyte-flow-cytometers/specifications/7syb.qB.D6MAAAFBV7o7FnRb,nav;pgid=WZtMKfaYs81SRpEoh9VgbI720000CVPV_BBr;sid=PkPRmcIRQ1_emZUkxcfBESxEh8UTxgGbg-NYIv436iSRwUp_5oE3LgZPVeQAlXodKzH_gBFn_X4oMZfvewXUpohLXOJVkMcVd4OD_HWFx2Bh78hq5ZpOWn9X5RVu417NYgP_gBFnti0JWwEsx-uzOEYY

http://www.emdmillipore.com/Web-US-Site/en_CA/-/USD/ShowDocument-Pronet?id=201601.186

ACEA NovoCyte 1000 $40K ?
http://www.aceabio.com/products/novocyte/
Novote Cyte model 2000, 3000 have more optins.

BeckmanFlow.com CytoFlex
http://beckmanflow.com/?page_id=379/?pi_ad_id=105930129160

Accuri C6PLUS  $49K

EmdMillipore Muse: $15K
http://www.emdmillipore.com/US/en/life-science-research/cell-analysis/muse-cell-analyzer/assays-for-muse-cell-analyzer/cell-health-assays-for-muse-cell-analyzer/2nab.qB.Jp0AAAFQ46hauq.k,nav#mch100102
Con: Closed system. Cannot be modified ?

Attune NxT Flow Cytomer

Stratedigm FLow Cytometer

http://www.ncbi.nlm.nih.gov/pubmed/16680701
http://www.biocompare.com/Editorial-Articles/167700-What-To-Look-For-in-a-Personal-Flow-Cytometer/



Sales rep from BD on Gallios and CytoFlex
As per my voice message, I understand you are looking for a quote for 6 color Gallios Flow Cytometer, but we now have a new, much smaller flow cytometer with greater capability than the Gallios, and less expensive.   It is called the CytoFLEX Flow Cytometer.   The CytoFLEX is available in 21 different configurations from a 1 laser/4 color system to a 3 laser/13 color system in a small box (16in x 16in x 13in).   It is completely upgradable to any configuration at any time.   A 96 well plate loader option is available as are 561 nm and 375 nm laser options.   Independent testing has proven this instrument to be one of the most sensitive instruments in the market today.
 If the 561 or 375 nm lasers interest you, please let me know and I will forward additional information on our CytoFLEX “S” System.

Wednesday, April 20, 2016

bio125 20160420 flow cytometer data analysis in R,

Section 3
video recording

9:10-10:10am, Flow cytometer data analysis in R using my own laptop. Helped some students with RStudio package installations.

Problems: In Windows 10, Rstudio has to be run as administrator to install packages.

10:15am, course evaluation
10:25am post-computing survey
10:35am lab 11.1_group

section 4

1-2pm. R Rstudio on flow data anlysis
Problems: R3.2.3. installation.  a/s/n warning.   Jumping lines. Setting working direcories.

2:11pm. Post survey

by 3pm.  review bioinfor_1






Tuesday, April 19, 2016

toread, yeast RLS screen paper



http://www.cell.com/cell-metabolism/abstract/S1550-4131(15)00465-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1550413115004659%3Fshowall%3Dtrue

toread, Yeast longevity promoted by reversing aging-associated decline in heavy isotope content


Yeast longevity promoted by reversing aging-associated decline in heavy isotope content

stochastic modeling of histone modification in yeast


mating phenotype maintenance?

CR SIR2 histone modification modeling

Reference:
J Xing's similar work on histone modification


CR, rapamycin effect on LOH in CLS and H2O2 treatment, NIH R15?



CR, rapamycin effect on LOH in CLS and H2O2 treatment

Human essential genes?

Mining  shalem 14 data set

References: NEST in in shirley liu's lab.

Project Achilles
http://www.broadinstitute.org/achilles

Monday, April 18, 2016

*** human essential gene

NEST, sherley liu lab,
http://nest.dfci.harvard.edu/


CRISP screen paper from Feng Zhang lab:
http://www.ncbi.nlm.nih.gov/pubmed/24336571

Try to load the xlsx file into Rstudio. I waited for more than 50 minutes on Byte (4 G RAM), I then have to kill it. I then converted the xlsx to csv, and it worked in less than 1 minute!!!


> length(unique(tb$sgRNA.sequence))
[1] 64751
There are 64.7K CRISP shots.

Only 18.7K genes are tagged. So, the missing one contain essential genes. Some other criteria are needed. 
> length(unique(tb$Gene.name))
[1] 18736

.gitignore file


.gitignore


https://git-scm.com/docs/gitignore

Resazurin Cell Viability assay


http://www.cellsignal.com/products/cellular-assay-kits/resazurin-cell-viability-kit/11884

Elastic net regression


Elastic net regression

http://www.r-bloggers.com/kickin-it-with-elastic-net-regression/

***, compound profiling, initial thoughts

These compounds are 'newly designed and synthesized' and their targets are needed to be identified and verified.

PCA, then, Euclean distance,  MCL
PCA, then K-means

For comparison: Elastic net

Score criteria: jaccard index with original annotation.

https://en.wikipedia.org/wiki/Jaccard_index

Friday, April 8, 2016

bio125 cancer and ucsc genome broswer


Section 3:
2015 bio125 assignments are based on GRC37/hg19 assembled in 2009.
4 exercises in class
10:30am, class is over.


Wednesday, April 6, 2016

bio125 HU treatment of yeast cells


Get the HU experiment start as quickly as possible.
During the 1.5 hour incubaion time,
check FOA plate, take pictures
go over group exercises. 


Section 3:
Projector is set at a wrong station. A technician came and figure it out. 





During the incubation, flip tube occasionally to make sure cells are suspended. 

HU made cells arrested at G1 phase with round shapes. 
 
Section 4:

Problems: Because we did not sonicate the cells, so often cells in G1 phases are often chained together.  It is easy for students to count big circle with tiny dots as S phases, and everthing else as unbudded.
 
References
http://hongqinlab.blogspot.com/2015/04/bio125-hydroxyurea-induced-g1-arrest.html
http://hongqinlab.blogspot.com/2015/03/hydroxyurea-treatment-of-yeast-cells.html
https://youtu.be/yxA1-MvwZfQ  2014 HU video


Tuesday, April 5, 2016

bio325 guest lecture, yeast oxidative stress analysis


Try to lead students work on Rmd file for yeast gene expression data analysis

It turns out that the bioconductor packages are not supported by the recent R3.2.4. I had to lead students to use R3.2.3.

Among the students, there are 7 Apple laptops and 2 windows laptops.

I made a mistake when going through probes on Affymetrix Yeast 2.0 chip. It contains 2 MSH2 genes, on for S cerevisiae and one for S pombe.


Saturday, April 2, 2016

23andMe in courses

23andMe in courses

Udacity course
https://www.udacity.com/course/viewer#!/c-bio110/l-301595193/e-302316765/m-302316766

MSH2, DNA mismatch repair, and sporadic colon cancer


BIO125 used MSH2
A Howard U and Johns Hopkins study on sporadic colon cancer and DNA mismatch repair
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713502/


Primer design to amplify your DNA signature, identify RE to distinguish the polymorphic sites.




open human, data source


https://www.openhumans.org/

Personal Genome Project,

Personal Genome Project

https://my.pgp-hms.org/public_genetic_data?data_type=23andMe

Why the data vary from 5M to 200M?

spelman biology curricula

Competence-based core curriculum. reading, writing, talking and doing science.

SAWOK, science as a way of knowing
http://www.spelman.edu/docs/academics-biology/bio_sawok-classes_spring2012.pdf?sfvrsn=0

Morehouse
http://www.morehouse.edu/academics/bio/pdf/Biology-Dept-Handbook-082514.pdf


Gene and genealogy resources
http://dna-explained.com/category/education/

23andme Data Format, technology



The file 23andme provides has four columns: 
rs ID, chromosome, position, and genotype


Beadchip for genotyping
https://www.23andme.com/more/genotyping/

Bioconductor 23andme


http://www.vincebuffalo.com/blog/2012/03/12/using-bioconductor-to-analyze-your-23andme-data.html


Friday, April 1, 2016

bio233 order list fall 2016

Wish list for bio233 orders

** marker pens
** 10 tally counters
** 95% enthanol large order for 70% enthanol bottle
**latex-free gloves
** lens cleaners

swim noodles
colored bacteria for edutainment

cover slips, fix

slides for gram stains: spirilum +/-, bacillus +/-, cocci +/-

x brightline hemacytometer chambers

scissors
scotch tapes
play doughs


nutrient plate agars

small bottles for ethanol. Idodine. Crystal violet.

Yeast selective media, drop-out media

bibulous papers
filter papers

BPB pH color indicator for fermentation lab. 

BD Calibrite beads

15ml falcon tubes


2016 research day preparation

Research posters:
Maya Jones
Faith Lyons
Maya Bryant
Jessica Corley


BIO125 course posters
Gaina-Yvvan Pierre, Elsie, Unique Hayes
Jaliyah Peterson, Lady Nwdike


Oral presentations:
 Kierra Parker
 Imani-Michelle White

bio125, 20160401Fri FOA

Materials: FOA plates, cells, serial water, Eppendorf tubes.

Section 3:
Ask the purpose of URA3 and FOA,
9:20, draw a diagram on the board. 
Go over previous student mistakes, not mix cells well, label the cover, adding cells to the cover. 
9:30, students started the lab. Students should have 9 tubes, and can be balanced triangularly in centrifuge. 
9:47. Students cannot see the pellet for OD=0.01. I remind them to orient their tubes the same way, so they can know where the pellet positions, even they cannot see the pellet.
One group only labeled OD on the tube but not strain names, and are confused after centrifuging
by 10:30, four groups are still working on the lab, because they have to redo the dilutions.
Forgot to ask students to label their section, and group on plates.




Section 4:
Emphasize that tubes during spin should be arranged 

One group was not sure that tips need to be changed each time for a different dilution.



Reference:
http://hongqinlab.blogspot.com/2015/04/bio125-foa.html
http://hongqinlab.blogspot.com/2014/03/bio125-foa-assay-of-msh2-mutants.html