Friday, May 30, 2014

RISE START projects, ASPIRE project, summer 2014

Hierarchical clustering analysis

Metric survey data analysis

Network robustness

NIH R25 short coures on mathematcal, statistical and computational tools for studying biological systems

Short Courses on Mathematical, Statistical, and Computational Tools for Studying Biological Systems (R25)

Thursday, May 29, 2014

network hSNP, CNV note

CNV genes show no SNP with frequency from Bio-Q and Ensemble.

Monday, May 26, 2014

SAT score by states 2013

Thursday, May 22, 2014

Volunteers need for a two-day Python programming bootcamp at Spelman College

Experienced Python programmers are needed to work as TAs for a two-day Software Carpentry Bootcamp at Spelman College on June 10-11, 2014.

This two-day bootcamp is scheduled to have 1/2 day on shell programming, 2 half-days on Python programming, 1 half-day on version control using Git. Software Carpentry lesson can be seen at  TAs do not have to volunteer for two days.

Please contact hqin at spelman dot edu if you can.

Journals, annual research and review in biology

Dear Colleague,

Annual Research & Review in Biology (ARRB): ISI Thomson Reuters indexed journal:

Annual Research & Review in Biology (ARRB) (ISSN: 2347-565X) (Previous name: Annual Review & Research in Biology, ISSN: 2231-4776)

ARRB is an OPEN peer-reviewed INTERNATIONAL journal. We offer both Online publication as well as Hard copy options. Article Processing Charge is only 100 USD as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). We are delighted to inform that record 5844 submissions were received in 2013 by SDI journals (199.4% growth from last year) (Link).

2. Transparent and High standard Peer review:
In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system (Example Link1Link2Link3Link4Link5, etc.). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by our comment section.

3. Proposed Time Schedule:
Submission to first editorial decision with review comments: 3 weeks
Submission to publication: 6 weeks
State-of-the-art ‘running issue’ concept gives authors the benefit of 'Zero Waiting Time' for the officially accepted manuscripts to be published.

4. Abstracting/indexing:
Many respected abstracting/indexing services covered our journals.
HINARI (United Nation's Database)
EBSCOhost (USA) (Mail confirmation link)
AGORA (United Nation's FAO database)
Chemical Abstracts Service (“CAS”) (Mail confirmatiom link)
For more information please visit here

5. Authors’ profile:
Considering high peer review standard, quality control, etc. our journals have been chosen by academicians of many famous universities, institutes, etc. A glimpse of authors’ profile is provided here.

6. Testimonials:
Appreciation of our esteemed satisfied authors is the greatest inspiration behind the hard-work of our editorial team. Some of the testimonials are available here.

7. Article Processing Charge (or Publication Charge):

Article Processing Charge (or Publication Charge): Manuscript submitted within 01 April, 2014 -- 30 June, 2014 will be eligible for 80% discount on normal Article Processing Charge (APC) of 500 USD. (i.e. Effective APC: 100 USD). For more information visit here.

7.1. Reprints (Hard copy ):
Hard copy are also available at extra cost. For detailed information please see here (Reprint information link).

8. Sample papers:
and many more…

9. Highly qualified Editors:

Dr. George Perry, Dean, College of Sciences, University of Texas at San Antonio, USA. (One of few authors having more than 24,000 citations).
Dr. D.N. Wheatley, President, International Federation of Cell Biology, Aberdeen, UK.
Prof. Luis Colom, Director of Center for Biomedical Studies, University of Texas at Brownsville, USA.
Prof. Olufisayo Jejelowo, Director for the NASA URC Center, Texas Southern University, Texas, USA
Prof. Andrew Tsin, University of Texas at San Antonio Texas, USA.
Prof. Hans Vliegenthart, Bijvoet Center, Utrecht University, Utrecht, The Netherlands
Prof. Gemma Casadesus, Department of Neurosciences, Case Western Reserve University
Prof. Hyoung-gon Lee, Department of Pathology, Case Western Reserve University
Prof. Vladimir Matveev, Lab of Cell Physiology, Institute of Cytology, Russian Academy of Sciences, Russia

10. Manuscript submission
Option 1:
Online submission (recommended): Subcentral (
Option 2:
Email attachment to the editorial office at 
To download MS word SDI paper template click here
To download SDI Manuscript Submission form click here
To download Latex paper template click here

Best regards,
Ms. Samapika Mondal,
Annual Research & Review in Biology: ISI Thomson Reuters indexed OPEN peer reviewed journal
Reg. Office:
UK: SCIENCEDOMAIN international, Third Floor, 207 Regent Street, London, W1B 3HH,UK,Registered in England and Wales, Company Registration Number: 7794635, Fax: +44 20-3031-1429
USA: SCIENCEDOMAIN international, One Commerce Centre, 1201, Orange St. # 600, Wilmington, New Castle, Delaware, USA, Corporate File Number: 5049777, Fax: +1 302-397-2050
India: SCIENCEDOMAIN international, U GF, DLF City Phase-III, Gurgaon, 122001, Delhi NCR, Corp. Firm Registration Number: 255 (2010-11), Fax: +91 11-66173993
Disclaimer: Annual Review & Research in Biology’ continued as ‘Annual Research & Review in Biology’ from Vol.4, Issue 1 (Jan-March, 2014). This journal has no connection with any society or association, related to Biology and allied fields. This journal was not and is not associated with Annual Reviews, Inc. Authors and visitors are kindly requested to note that ARRB is an independent journal run by SDI.

You have received this e-mail in the genuine belief that its contents would be of interest to you.

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College retreat

May 22, 2014, 9am->4pm 
Loudermilk Center 
40 Courtland Street, NE
Atlanta, Georgia 30303

Wednesday, May 21, 2014

HP color laser jet to Maverick laptop.

HP lasterjet color M551 driver is recognzied by Maverick.

Add printer by IP, and the driver is recognized.


Tuesday, May 20, 2014

dbSNP ftp site


Moodle 2.5, trainining

Major changes:
Drag and drop uploading
Book publisher's IMS content package

My Private files: available in all courses under my account.

Conditionally access resources: Click syllabus and then complete the next assignment. 

Course completion check. 

Questions: 50M is the maximal size for uploading file? 

Saturday, May 17, 2014

Github DOI setup and educational discount, todo

Todo: Need to generate DOI for R comp biol repo.

orders, bio386

calibur beads

Monday, May 12, 2014

instructional software request to install



Respondus locker browser

FASEB MARC faculty/mentor travel award

two students

One form

response heard within days

x Chair support letter

Statement of understanding are emailed to me and the two students. Everyone signed, with a copy of ssn card.

Friday, May 9, 2014

Reflection on performance of multiple choice questions in exams

For four-choiced question, if the error rate is around 75%, it indicates that the 4 choices are randomly selected. On the other hand, an error rate over 90% indicates that a wrong choice was preferred by most exam-takers.

So, around 75% error rate indicates that exam-takers are basically clueless, whereas over 90% error rate indicate a mis-understanding.

Wednesday, May 7, 2014

Location of Software Carpentry Workshop, Spelman College, June 10-11, 2014

Driving direction to Spelman College main entrance.
Spelman College
440 Westview Dr. S.W. 
Atlanta 30310

(Note that GPS of the Spelman mailing address will lead you to the pedestrian entrance)

Albro-Falconer-Manely Science Center, Room 232, Spelman College
(Building 19c on Spelman campus map. AFM Science center is located at the rear-right corner of the campus from the parking lot. )

bio233, materials to order, for Fall semester, 2014

95% ethanol large bottle
nutrient plate agar
small bottles for ethanol. Idodine. Crystal violet.

bibulous papers
filter papers

slides for gram stains

one roll of parafilm

BPB pH color indicator for fermentation lab. 

calibur beads

brightline hemacytometer chamber

QIAGEN DNA purification kit

zymo kit, plasmid kits

Spelman Letter grade scale

Tuesday, May 6, 2014

multidimensional scaling in R

Journal of Biology and Medicine, todo

As part of our continuing mission to enrich the sharing of ideas between medical and scientific communities around the world, 
Journal of Biology and Medicineinvites contributions from researchers related to Biology and Medicine.

We strongly believe that this potential research in the field of medicine would be beneficial to the people working in this field.

Thus on behalf of Journal of Biology and Medicine, we invite you to present your view on your research as a short note/ mini review/ full review, for our upcoming issue (Volume 6, Issue 2).

Submit manuscript at: or

We would truly gratify and appreciate receiving your submission. We are waiting for your Quick and positive reply.

For any other queries please feel free to contact us.

With thanks
Koyada. S
Associate Managing Editor
for Editor-in-Chief
Journal of Biology and Medicine

Monday, May 5, 2014

TeamViewer on osX

Install TeamViewer on a mac server.

It gave "Your ID" and "password".

On a client computer, I installed TeamViewer. Entered the TeamViewerID on the server, followed the password, and it worked.

Remove logmeIn from MountainLion

cd /Library/Application Support/
sudo mv  LogMeIn\ Plugin  LogmeIn\  Plugin.toRemove
sudo mv  LogMeIn  LogmeIn.toRemove

cd /Application
sudo mv

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.

Friday, May 2, 2014

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 or as e-mail attachment to the Editorial Office at
For more details on submission process and manuscript preparation please click