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by ivan

A talk by Dr. Skinner May 16th

May 14, 2014 in Labwide Announcements

Just a little reminder about the talk we will have on Friday.

It is by Dr. Michael Skinner, who's big claim to fame (?) is that non-genetic mechanisms can produce inheritable traits (i.e. chemical modifications that do not change the DNA sequence). I shall not pass any judgement (even though this disclaimer makes my bias obvious). The article attached tells a good story about his research, its implications and reception.

Please read this: Skinner Science

As one of the not-so-many evolutionary biology labs on campus, I believe that we should be able to ask a few provocative questions this Friday.

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by arnab

Combined Annotation–Dependent Depletion

May 11, 2014 in Labwide Announcements

Following up,

I will be discussing the paper CADD published not so long ago in Nature Genetics http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html, which implements a hyper-plane support vector machine trained to rank pathogenic variants in the human genome. The discussion will take place on friday, May16 from 3:00 pm to 4:30 pm

-Arnab

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by aaron

Random Walks in Gene Space

May 11, 2014 in Labwide Announcements

Gentleman,

I will be leading out in a discussion on Sahinalp's paper on random walks and driver genes, May 13 if anyone is around.

Here is the paper: HitNDdrive-Sahinalp-2014

 

-aaron

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by ivan

A few curious papers.

April 3, 2014 in Ivan's Blog, Labwide Announcements

Here are a few intereseting recent development that have happened in the past week:

1) The paper I would like to talk about next Thursday: http://www.pnas.org/content/early/2014/03/19/1220873111

2) A paper about "machine teaching": http://www.tandfonline.com/doi/abs/10.1080/09540091.2014.885279#.Uz3HInXqfbg

3) A paper on differential gene expression detection: http://www.biomedcentral.com/1471-2105/15/79

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by Jason

Detailed analysis of Neanderthal genomes

December 18, 2013 in Jason's Blog, Labwide Announcements

Svante Pääbo's lab has just published a detailed analysis of the newer high-resolution Neanderthal genome sequences! This is very exciting and worth a look; someone, maybe me, should present this paper in lab meeting in January.

See the paper here.

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by ivan

A simple bridge between perl and C++

November 5, 2013 in Labwide Announcements

I have created a simple example script that wraps around the perlapi. This allows perl code to use C++ functions. There are a few accessory functions, that allow to convert a perl array into a c array and back. This may require a little cleanup so that it's not mandatory to de-reference the array in perl.

Hopefully the code is not too hard to understand. I would like to give a quick rundown of this on the Friday meeting if possible - it seems like a few people can benefit from this.

I will also write a short blogpost on my blog, and let you know when that's done.

The code is hosted here.

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by Jason

Machine Learning Toolkit, Mahout

November 3, 2013 in Labwide Announcements

For anyone who's project or interests touch on machine learning, I came across the Apache project Mahout. It focuses on scalable implementations of machine learning algorithms, and appears to have a pretty active user community. It's written in Java.

The main project site is: Apache Mahout.

There is also an article about it in the current issue of Dr. Dobbs (the programming magazine).

mantle-mahout

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by Jason

Welcome to New People!

August 13, 2013 in Labwide Announcements

Starting this fall we will be having @arnab and @chenzhe in the lab full time, and @ivan will be joining us as a research assistant. Welcome everybody!

Please note that there is an Orientation forum on the private lab intranet that has some useful information on getting set up with computer accounts and such.

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by Jason

Advice for Programmers

July 16, 2013 in Labwide Announcements

Two nice resources here that discuss best-practice programming guidelines.  The first is an article in the current issue of Dr. Dobb's Journal (an old and good programming magazine): Advice to a New Programmer.  In a nutshell:

  1. Read a lot of code.
  2. Learn your tools thoroughly.
  3. Plan your code before you write it.
  4. Write lots of code and have it reviewed.
  5. Write tests as you code.

The second is an article that I put it one of the shared Dropboxes but is worth resharing: Best Practices for Scientific Computing.  The advice in brief:

  1. Write programs for people, not computers.
  2. Automate repetitive tasks
  3. Use the computer to record history.
  4. Make incremental changes.
  5. Use version control (like GIT).
  6. Don't repeat yourself (or others).
  7. Plan for mistakes.
  8. Optimize software only after it works correctly.
  9. Document design and purpose, not mechanics.
  10. Collaborate.
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by Jason

Great Educational Resources!

July 5, 2013 in Labwide Announcements

Updating my previous post, I came across a nice series of lectures on YouTube on statistics-related topics that are really excellent.  I also found a couple of tutorials on understanding and analyzing Next-Generation DNA Sequence data and on programming for Bioinformatics that seem very good.

I've listed all of these tutorials in the Forums, under Educational Resources and Webinars.

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