Author Archives: ilknur

Fascinating World of Molecular Robotics

Note: an extended version of this post is on medium here On September 21st 2018, I spent the entire day at 9th Annual Wyss International Symposium. The topic of this year was Molecular Robotics. I admit that this is not … Continue reading

Posted in Molecular Robotics | Leave a comment

Medical Imaging with Deep Learning (MIDL 2018) Conference: What is Hot?

Last week, I dived into the world of rejected extended abstracts from the first ever deep learning conference focused on medical imaging (MIDL 2018) organized in Amsterdam this summer. This week I am in the mood for the opposite end, … Continue reading

Posted in Deep Learning, Medical Imaging | Tagged , , | Leave a comment

Medical Imaging with Deep Learning (MIDL 2018) Conference: Exploring Rejected Extended Abstracts

Nowadays, everybody and their grandmothers (and grandfathers) are utilizing deep learning for medical imaging problems. This has now become a hot industry. Even though major computer vision (CVPR etc.) and medical imaging conferences (SPIE,ISBI,MICCAI) are currently dominated by deep learning … Continue reading

Posted in Deep Learning, Medical Imaging | Tagged , , | Leave a comment

Coursera’s Systems Biology and Biotechnology Specialization – My initial impressions

Couple years ago, Coursera started offering a series of courses in Systems Biology developed by the Icahn School of Medicine at Mount Sinai in New York. The series includes 5 lecture style courses possibly recorded in 2013/2014 (as per the … Continue reading

Posted in Dynamic Systems, MOOCs, Systems Biology | Leave a comment

Instructional Technology Tool using Adobe Flex

At one point in my academic life, I worked as an Instructional Technology Fellow helping faculty members design online/hybrid courses. When I saw Andrew Ng’s Stanford Machine Learning lectures online, inspired by my job, I wanted to build a tool … Continue reading

Posted in Demos, Instructional Technology | Tagged , | Leave a comment

Central Pattern Generators to Synthesize Birdsongs

Songbirds are among the most interesting creatures of nature. Out of 10,000 bird species, around 4,000 are songbirds. They sing for reasons such as territorial ownership and mating. The young birds learn their songs by listening to a tutor. This … Continue reading

Posted in Algorithms, Demos, Dynamic Systems | Tagged , , , | Leave a comment

Machine Learning web service using Python,Bottle and Scikit-Learn

Software as a service (SAAS) is a nice way to provide analytics capabilities to people who are not experts in machine learning and/or do not have time to build the necessary tools. Here, I implemented a simple web service utilizing … Continue reading

Posted in Demos | Tagged , , | Leave a comment

Needleman-Wunsch pairwise DNA sequence alignment RESTful Web Service

Here is a RESTful web service that provides global DNA sequence alignment implementation as a service. See my post on the algorithm itself. Download .war archive with java source code if you would like to install it yourself. The service … Continue reading

Posted in Algorithms, Demos | Tagged , , , , | Leave a comment

Needleman-Wunsch algorithm for DNA sequence alignment (2 sequences)

Update (May 26th 2014): See the RESTful web service implementation of this algorithm here Given two DNA sequences, you are asked to align these two sequences where for each non-matching nucleotide pair you will be penalized by 1 point and … Continue reading

Posted in Algorithms | Tagged , , , | Leave a comment