2015年のまとめ

I wish you a happy new year. WordPress.com 統計チームは、2015年のあなたのブログの年間まとめレポートを用意しました。 概要はこちらです。 ニューヨーク市の地下鉄には1,200人が乗車できます。2015にこのブログは約7,600回表示されました。ニューヨークの地下鉄に置き換えると、約6台分になります。 レポートをすべて見るにはクリックしてください。

down load images from web.

Web crawling technology is useful for getting broad range information. There are lots of document about web crawling using python. Today I used scrapy for crawling. Scrapy is open source framework for web crawling. The library can be installed using pip install. After installed scrapy, I started following command. Then imagedl folder was cleated and

Integration RDKit and Knime using Python scripting node.

Knime is tool for making workflow. Old version of Knime can’t call RDKit from python scripting node directory. New version of Knime and python scripting node can do that. It’s means that user can build more flexible work flow. ;-) I set up my environment and test it. At first I installed new version of

Compare chainer example with GPU and without GPU.

Some days ago, @fmkz__ -san posted about chainer. http://blog.kzfmix.com/entry/1450445178 I have not ran example code, so tried it. At first, Run with out GPU. Next, Run with GPU. Only add option ‘–gpu=0’. 3 to 5 times faster with GPU than without GPU.

Seed up of array calculation.

My colleague in CADD team told me that to calculate massive data in python, his recommendation is numpy. And he showed me very nice code. ( Nice stuff. ) Numpy is the fundamental package for scientific computing with Python. It can handle data as vector, array. That means native python handles Ns list data with

Find MCS in R

Find maximum common substructure is useful for finding core scaffold. I think that finding MCS, using commercially available tools is common (pipeline pilot ?). I often use RDkit. ;-) Today I found the library that search MCS in R, named fmcsR. That’s sounds nice, because if fmcsR works fine, I’ll implement the library to Spotfire

mishima.syk #7

Yesterday, Mishima.syk #7 was held. It was really impressive for me. Thanks to all participants and presenters. I also presented demonstration about “Chainer” and “Tensorflow” in QSAR. My presentation was uploaded to github. https://github.com/iwatobipen/mishimasyk/tree/master/mishimasyk7 In my opinion, Using DL for QSAR is good idea but still challenging. Because there are some problems. 1st. Kinds of

Hit triage, case of MTase

I often see keyword “PAINS” in literature . Frequent hitters of HTS deck are problematic and PAINS filter is useful to remove them because false positives are time and cost consuming. Researcher of Lilly, reported nice letter in J. Med. Chem. Lett. http://pubs.acs.org/doi/abs/10.1021/acsmedchemlett.5b00375 The author analysed there HTS campaign of Methyltransferases( MTase ). They screened

Make password input box using Tkinter.

I met python about 5 or 6 years ago, but I have never written a code using Tkinter. Main reason is that I often call function from CUI or Web UI, so I didn’t need GUI. But, some days ago, I want to make a plugin that need password box GUI. So, I searched google

New function of rdkit

To design new small molecule, we often consider about shape of molecule. Molecular conformation analysis is difficult but important task. Because small molecule is too flexible. Gregory. A. Landrum( developer of rdkit ) reported new function of conformation generation in J. Chem. Inf. Model. http://www.ncbi.nlm.nih.gov/pubmed/26575315 The author developed two functions called Experimental Torsion Distance Geometry