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Comment Re:Python (Score 1) 465

a complete answer would be Python and C++, because numpy/scipy can't do everything and Python is still very slow for number-crunching.

The problem with using the mix (when you actually write the C++ code yourself) is that debugging it is a major pain in the ass

+1 "I just spent three days chasing down build error that uses numpy/scipy"

Comment Re:Python (Score 1) 465

I have a friend who works for a company that does gene sequencing and other genetic research and, from what he's told me, the whole industry uses mostly python.

I work in a Gene Sequencing company and the current debate is: Python vs Clojure vs Scala:
Python unquestionably has the best bioinformatics support. Period. No debate. But the lack of language features has irked many programmers, myself included.
Clojure is gaining attention as a pure functional language with an R-like environment for large scale machine learning tasks. (Bioinformatics is machine learning applied to biomedicine). This makes porting Matlab/Octave/R code much easier, or so the thinking goes.
Scala has its backers. Java is nearly invisible in the bioinformatics world, but the JVM is hard to ignore. Scala has excellent support for Machine Learning but terrible support for "biological and medical applications". Hat tip: you can hire scala programmers or teach Scala to Java programmers in short time

BIG DATA is a bigger problem for us today than previously:
"genome wide arrays" used to mean all ~25,000 gene transcripts or 500,000 single DNA changes (SNP).
These revolutionary technologies are already considered "old".
The rise in performance and drop of cost of DNA sequencing is much faster than the commodification of CPUs during the internet dot-com race .

Comment AMD = case study in good engineering, bad biz dev (Score 1) 188

Recall when AMD first had 64bit support and intel was still doing *EMULATED* 32bit. AMD was hands down the best option. Either AMD biz dev was bad, or Intel biz dev was good (illegal?), or both. I suspect it was both. Having one CPU maker is bad for everyone. Long live AMD, I guess.

Comment Re:you have the source (Score 1) 566

How would they detect any shared properties?

Perhaps Covariance analysis? (mutual information, pearson, svd, etc).

Input: 3 data streams A,B,C each which are not truly random
Correlate: A&B, A&C, B&C
Subproblems: given A&B predict C
Subproblems: given A&C predict B
Subproblems: given B&C predict A

NSA has mathematicians better than I, for sure. My guess is that if an agency has altered an RNG then they have done so in a way that is systematic. These kinds of problems are common in analysis of complex systems -- given three non random variables with characteristic variance can you predict the output variable from the covariance? I dont think I could, but it seems feasible to me that the NSA could.

Comment Re:Here's your debate (Score 1) 566

NSA employs more mathematicians than anyone.
NSA uses linux for their data farms.
NSA is a code breaking agency.
NSA has worked with many tech companies, from wintel to google, stellar wind to TIA, etc, etc.

Occam's razor: which is more likely?
A) NSA worked with intel to provide a known hardware key OR
B) NSA did not work with Intel and chose instead to work with Microsoft, Google, Yahoo, Verizon, ISPs, etc, etc, etc

A is more likely.

Comment Re:you have the source (Score 1) 566

Entropy + mutual distrust = security
I would have never thought
MSS+KGB+NSA = privacy IFF every agency provides a mutually distrusted hardware key

But is this mathematically true? (honest question)
Shannon entropy also applies to mutual information
, which formally includes joint entropy, eg...."detecting when values change together".
If these same agencies were able to detect any shared properties (such as joint entropy), the encryption would be EASIER to break, not harder.

Comment Doesn't this give EFF standing to sue? (Score 1) 225

Previous court cases were thrown out because no one could prove they were being spied on. PERFECT ! Either: A) FBI can install equipment using by citing authorizations which gives ISPs and customers grounds to sue ...or... A) FBI cannot install equipment because they have cited no authorization to do so. SO which is it FBI? Are you, or are you not installing equipment? ** Fuck sports. GO TEAM EFF !!!! **

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