Including RStudio, XPPAUT, PPLane etc.
https://qubeshub.org/resources/software
Tuesday, April 26, 2016
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
Discipline-Based Education Research: A Guide for Scientists Paperback – July 16, 2015
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.
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
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
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
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 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
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
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
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