bio125 final exam.

Five students finished the 40-question closed book part in 1 hour.
Most students spent 50-70 minutes on the 12 question bioinformatics section for their first attempt. Student usually spent very short time on their second attempt.

There are 12 questions in the open book part, I set the total score to 10.  I found this mistake after students submitted their answers. I adjust the total score to 12 while students are still taking the exam, the grades are updated and Moodle did not complain.

By 1pm, only 3 students are left.

Journal of Data Mining in Genomics and Proteomics

On behalf of editorial board of Journal of Data Mining in Genomics & Proteomics we invite you to submit a manuscript or review to be considered for upcoming issues.

We would like to bring to your kind notice regarding the upcoming special issue for the year 2014.

Special Issue Title Handling Editor Bioinformatics for High throughput Sequencing UlliWeier, Lawrence Berkeley National Laboratory, USA Data annotation and Management Maria Krestyaninova, Wellcome Trust Genome Campus, UK Datamining in the Cloud Jennifer Dommer, National Institutes of Health, USA Integrative Biology: Lupus Nephritis Tianfu Wu, UT Southwestern Medical Center, USA Protein Modelling SonaVasudevan, Georgetown University, USA Systems Biology : Biomarker Discovery FirasKobeissy , University of Florida, USA Bioinformatics Tools and Techniques: Datamining SuparnaMitra, University of Tuebingen Germany Algorithm Evalution and Validation in Proteomics Tamanna Sultana, University of Pittsburgh, USA Algorithms for Molecular Biology TurgayIbrikci, Cukurova University, Turkey Genome Annotation Jorge Cancela, Technical University of Madrid, Spain

You may submit your paper online at http://www.editorialmanager.com/omicsgroup/ or as e-mail attachment to the Editorial Office at editor.jdmgp@omicsonline.org

For more details on submission process and manuscript preparation please click http://omicsonline.org/instructionsforauthors-data-mining-in-genomics-proteomics-open-access.php

Li Ma defense, haplotype, Qing Song lab, Morehouse medical school

Fu and Ma in prep


Teri manlolio,

Schizophrenia, Lee 2012, GWAS
http://www.nature.com/ng/journal/v44/n3/abs/ng.1108.html

Smemo etal Nature 2014 longrage haplotype FTO IRX3
 http://www.nature.com/nature/journal/v507/n7492/full/nature13138.html


haplotyping methods
GMP 2001, nat genetics
Qiagen 2005
Polony2006, Nat Genet
Barcode 2009, Nat Method
Fosmid 2011, Nat biotech
HiC 2013, Nat Biotech
Illumina 2014, Nat biotech,


Laser microdissection of chromosomes, take half of 46 chrosomes, by chance we can get some single chromosomes which can be used for haplotyping.
23 chromosome is 3.5pg,  amplified to 5-8ug for highthroughput sequencing.
Use heterozygosity of identify diploid and haploid chromosomes.

HiFi software
http://www.cs.gsu.edu/?q=node/536

Quake Dataset
http://www.cbcb.umd.edu/software/quake/

How to zoom-in on selected coordinates in UCSC genome browser

To zoom in on a selected region, we can high-light a region and then select zoom-in.

Alternatively, we can type the chromosome number and coordinates into the search window:

In this example, we see introns

The dashed line of MSH2 locus indicate introns.



The blocks in this picture are exons with coding regions,

In the following picture, the circled regions are 5' untranslated regions, i.e., 5'UTR, because this region is at the 5' end of "ATG". Notice that 5'UTR is also in an exon.

teaching evaluation form

bio233, student project on antibacterial soap

1/10 dilutions of vwr, decon, and dial soaps. There are very viscous and hard to pipette.
70% ethanol as control.

I grew E coli overnight. Students spread 150 ul of Ecoli culture on LB plates. We then spot 5ul of each 1/10 diluted soap and 70% ethanol.

Bio125, go over midterm closed book exams.

2 hours, going over midterm exams. Finished about 30 questions.

Two student presented their project using the research day poster.

Bio233, virus trade off paper discussion

Two student led the discussion on De Paepe and Taddei 2006. The key figure 4 was not emphasized enough, and I jumped in and explained the figures.

todo: Journal of computational scinece education

http://jocse.org/submitProcedure/

XSEDE workshop, computational thinking

self-paced online tutorials
https://www.xsede.org/web/xup/online-training


https://www.osc.edu/~sgordon/

excel sliding bar

customize ribbon, developer

NameBox

https://www.osc.edu/~sgordon/workshop/materials

http://phet.colorado.edu/

VensimPLE

AgentSheet, shordor

Computational Science Competencies
http://hpcuniversity.org/educators/undergradCompetencies/
http://hpcuniversity.org/trainingMaterials/


inculcate

Moodle, regrading

Sometimes, questions are unclear, or wrong choices were picked as correct answer. Regrading is need in this case. After reedit the questions, 'regrade' can be clicked to reassign the grades.

bio125, western blot and signal detection.

We used 25K dilution of second antibody (jackson lab immuno), which is too high. Dr. Kioko said our Kodak Image System has not been optimized to detect Western blots. We need to optimize it during the summer.

bio233, epidemiology

show a video on john snow. the image is mostly still image, but the conversation is informative.

I asked students to go over wikipedia page on 1854 broad street cholera break. I then give John Snow's map to the students and ask them to draw conclusions. To explain clustering, I gave play dough to students and ask them to randomly drop playdough dots on the map. I then explained null hypothesis and alternative hypothesis, p-value.

I then went through slides with clicker questions inserted.

Class evaluation was administrated at the end of the class.

Bio125, hallmarks of cancer, mutagenic primer design

Western blot video. 

I showed students of Kioko's video on transfer procedures. 

1hr on Hallmarkers of cancer

1 hr on mutagenic primer design exercises.
Students have trouble to count the AA positions in alignment. I used subtraction to locate the positions. Students have trouble with offsets of counting.

Dr. Kioko did a demo on second antibody stain and HRP staining. He showed a chem-illuniance in the tube, and students recognize the light from the glow sticks. Kioko told students that they are mostly generated using the same principle.

Corrected a mistake in online quiz. Most students tried, but some did not. 

Design a mutagenic primer to engineer human C333F mutation to yeast MSH2

Goal: Engineer the human C333F mutation into yeast MSH2.

Link of video tutorial of this exercise:  https://youtu.be/SWgE_PfxmeU

Video on G548C is https://youtu.be/6C8E_OZKeeQ


The principle of site specific mutagenesis can be found in this tutorial video. Explanation of cognant sites can be see in this Youtube video.

Copy yeast and human MSH2 protein sequences in FASTA format from this link. 

Google "EMBL ClustalW2".  Then, paste the yeast and human MSH2 sequences in FASTA format into ClustalW2 window.

  After "submit", you should see the protein alignment.

Identify the cognant site in yeast MSH2. Human C333 corresponds to yeast C345.

Therefore, human mutation C333F should become C345F mutation in yeast MSH2 gene.



Now, we can design the mutagenic primer based on the DNA coding sequences of the yeast MSH2 (linked here).  You can copy-paste this sequences into ApE.

In the yeast MSH2 ORF sequence, the 345th amino acid position corresponds to 345x3=1035 nucleotide position. So, the codon position is 1033-1035.  We can select these 3 nucleotide in ApE to and double check this codon.

This selected codon should be:

We can verify that  codon TGC is amino acid "C".

To design a mutagenic primer, we will pick 10 bp left to the TGC codon and 10 bp right to the TGC codon, by select from 1023-1045.

Copy the selected sequence into a new ApE window.

At the center of this sequence should be "TGC".

The yeast codon usage table is:

The preferred codon for "F" in yeast is "TTT". 


We can manually change "TGC" to "TTT".

We can save this file in ApE as "C345F_mutagenic_primer.seq".