In 2018 we have developed a new Bioinformatics oriented web service that radically improves bioinformatics
education and research.
Bioinformatics is experiencing a reproducibility crisis. It has become challenging to understand
how analyses are performed and even more difficult to replicate the same processes again.
The Bioinformatics Recipes web application allows scientists to document,
execute and share data analysis scripts and the results of running these scripts.
We call these analysis scripts recipes.
The Biostar Handbook: A Beginner's Guide to Bioinformatics
The Biostar Handbook introduces readers to bioinformatics, the scientific discipline at the intersection of biology, computer science, and statistical data analytics dedicated to the digital processing of genomic information.
The Biostar Handbook delivers simple, concise, and relevant information for those looking
to understand the field of bioinformatics as a data science.
It is a comprehensive, practical handbook that covers all major
application areas of bioinformatics.
We are continuously updating the Handbook adding new chapters and sections to it.
Subscribe to our email list to be notified of these changes.
I teach the BMMB 852: Applied Bioinformatics course in resident instruction
in the Fall and online during the Spring semester.
Typically the course fills up very quickly once registration opens so please plan accordingly.
Schedule for Fall 2018 (Aug 20 - Dec 7):
Applied Bioinformatics, BMMB 852
116 Osmond Building
Mo/We 1:25- 2:15pm
This year's lecture notes are being designed as part of a new study book that is included in
the Biostar Handbook.
All students in BMMB 852 will be provided access to this resource.
I serve as director of the Online Graduate Certificate Program in Applied
Bioinformatics offered via the Penn State World Campus. The certificate builds
on courses developed for the Bioinformatics and Genomics Ph.D option at Penn
State with materials reworked for the online format. The Certificate requires
the completion of 4 courses (11 credits) and can be completed in a year.
I have worked and published in three distinct scientific fields: bioinformatics,
computer science and statistical physics. Lately I have been working mostly in
collaborations via the Bioinformatics Consulting Center. In this capacity I
advise and meet with students from a wide range of departments.
Five years ago I have created the Biostars: Question and Answer website that
runs on an open source software and aims to support and sustain scientific
communities. Today it serves over 2 million users a year and it has become the
most visited bioinformatics information resource in the world.
I have extensive software engineering experience having served as primary or
lead developer on numerous web based software pacakges. While I have certification
as a Java and XML developer currently I only program in Python (and occasionally C)
see also Python vs Perl:
Writing code is one of my passions.
Even this website is generated with a custom software
that I have written see: pyblue.
Bioinformatics Consulting Center at Penn State
I serve as the director of the Bioinformatics Consulting Center (BCC) at Penn
State. Our center offers bioinformatics data analysis services that cover
multiple application domains of high throughput sequencing. Services range from
routine data manipulation steps to developing novel, domain specific
methodologies. Our center is also in charge of distributing and managing the
sequencing data produced by the Penn State Genomics Core Sequencing Facilities.