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Re: [slightly OT] New O'Reilly book features Matz

Yukihiro Matsumoto

3/15/2007 3:05:00 PM

Hi,

In message "Re: [slightly OT] New O'Reilly book features Matz"
on Thu, 15 Mar 2007 15:47:48 +0900, "M. Edward (Ed) Borasky" <znmeb@cesmail.net> writes:

|programming". It was intended to get the programmer to create the
|documentation hand in hand with the code. However, literate programming
|has evolved into a concept I find very appealing -- so called
|"reproducible research." As practiced by the bio-informatics community
|in the R language, the core concept is something called a compendium. A
|compendium is a software package, which contains all of the code and
|data required to reproduce the research, including the tools to write
|the paper. The way it's done in R, and the way it could be done in Ruby,
|the author creates a collection of source and data files. The literate
|programming process of _weaving_ produces the document -- in the case of
|R, this includes running R scripts that do the analysis, create the
|figures, and so on.
|
|I think what I really would like to see is some combination of
|test/behavior driven development and reproducible research. In short,
|the programmer develops the tests, the software *and* the documentation
|concurrently.

Interesting idea. Where can I find more information for compendium
(in R)?

matz.
2 Answers

Alex Gutteridge

3/16/2007 12:29:00 AM

0

On 16 Mar 2007, at 00:04, Yukihiro Matsumoto wrote:

> In message "Re: [slightly OT] New O'Reilly book features Matz"
> on Thu, 15 Mar 2007 15:47:48 +0900, "M. Edward (Ed) Borasky"
> <znmeb@cesmail.net> writes:
>
> |programming". It was intended to get the programmer to create the
> |documentation hand in hand with the code. However, literate
> programming
> |has evolved into a concept I find very appealing -- so called
> |"reproducible research." As practiced by the bio-informatics
> community
> |in the R language, the core concept is something called a
> compendium. A
> |compendium is a software package, which contains all of the code and
> |data required to reproduce the research, including the tools to write
> |the paper. The way it's done in R, and the way it could be done in
> Ruby,
> |the author creates a collection of source and data files. The
> literate
> |programming process of _weaving_ produces the document -- in the
> case of
> |R, this includes running R scripts that do the analysis, create the
> |figures, and so on.
> |
> |I think what I really would like to see is some combination of
> |test/behavior driven development and reproducible research. In short,
> |the programmer develops the tests, the software *and* the
> documentation
> |concurrently.
>
> Interesting idea. Where can I find more information for compendium
> (in R)?
>
> matz.
>

There are some example compendiums here:

http://www.bioconductor.org/docs/papers/2003/...

and this paper is a good introduction:

http://www.bepress.com/bioconduct...

> "M. Edward (Ed) Borasky" <znmeb@cesmail.net> writes:
> I am actually hacking away on a project called Rameau to bring
> reproducible research to Ruby -- more the other way around,
> actually -- to apply the pragmatic automation of Ruby to the
> processes of reproducible research. I haven't spent too much time
> on it recently, but I'll assume neither you nor Matz is interested
> in volunteering to join it when I get more of it laid down and
> start looking for help. :)

Ed: I'd be interested in playing/helping with Rameau - have you
released anything yet?

Alex Gutteridge

Bioinformatics Center
Kyoto University

Ala

2/9/2011 3:53:00 AM

0


"Anonymous Infidel - the anti-political talking head"
<messiah2999@yahoo.com> wrote in message
news:8b33f117-47c7-449e-8170-e1aa211cac9f@g1g2000prb.googlegroups.com...
On Feb 3, 1:37 pm, Tracey12 <tracey12em...@gmail.com> wrote:
> Look what Obama has done!
>
> Unemployment up to 9.8 pct now!
>
> 48 Million on Food Stamps, the most ever!
>
> Gas prices rising
>
> Food up 15 pct!
>
> HOW'S THAT CHANGE WORKING FOR YOU NOW?
>Don't forget the record foreclosures coupled with record low home
>prices....

he is in good company if he is merely acting for the status quo

http://www.csmonitor.com/World/Global-Issues/2010/0618/G-20-summit-financial-reform-is-needed.-Bu...

G-20 Summit: Financial Reform Is Needed. But How Fast?
Friday 18 June 2010

by: Dan Murphy | The Christian Science Monitor


While most agree major change is needed - the term "radical reform" is often
bandied about by policymakers - they disagree on timing.

The divide between G-20 countries like the United States, which would like a
tough regulatory regime enacted soon to limit the ability of banks to
speculate in financial markets, and countries like France and Germany, which
agree with the approach in principle but want more time, echoes a debate
raging from Dublin to Tokyo.

For two years, industrialized nations have watched their deficits soar,
thanks to bank bailouts and stimulus spending designed to head off economic
free fall. The question now is whether it's time to rein in spending and
start reducing government debt. Some say yes, but others fear spending cuts
could fuel unemployment and drive economic growth down.

A key component of economic growth is lending, which boosts consumption and
encourages business expansion. But the mooted new rules would require banks
to hold more cash in reserve and lend less of their capital in hopes of
obviating the need for future government bailouts.

That, some critics say, could be another destimulative measure at a time
when countries across Europe are planning steep budget cuts.

"The argument is that this will very significantly add to the cost of doing
business, be passed on to the consumer, and reduce growth," says Uri Dadush,
a former senior economist at the World Bank who is now at the Carnegie
Endowment for International Peace in Washington. "There's a prima facie
argument that there will in fact be serious costs and that will have to be
balanced against the insurance that [governments] are buying against future
financial crisis." Banking industry's case

In mid-June, the banking industry made its case that regulation will
undermine growth. The Institute for International Finance (IIF), a
350-member group of most of the world's large banks, argued in a report that
the new rules would reduce economic growth by 3 percent in the US, Japan,
and Europe and cost more than 9 million jobs over five years.

"The point of this report is not to argue against regulatory reform," Peter
Sands, CEO of the UK's Standard Chartered Bank and an IIF official, told
reporters at the time. "But there is a price for making the banking system
safer and more stable, and that price will inevitably be borne by the real
economy ... the challenge is to strike the right balance."

At the moment, the balance being sought has to do with time.

The Basel Committee on Banking Supervision is a multinational body that
oversees standards set by the G-20 for global finance. The US, Britain, and
others have been calling for the new set of regulations, called "Basel III,"
to be implemented by 2012 - requiring banks to hold more reserves to protect
against losses and limiting how much they can borrow to speculate in the
credit default swaps and other derivatives that accelerated the financial
collapse that began in August 2007.

The measures are scheduled to be adopted at the second G-20 summit of the
year, scheduled for Seoul, South Korea. Analysts expect the meeting in
Toronto will provide hints of which way the leaders are going to jump in
November, but no hard-and-fast commitments.

"The sense I get is that the big game will be played in Seoul in November,"
says Dr. Dadush.

Dadush says that while he supports more regulation of banks, saying that
current "institutions are inherently unstable," he worries that it is being
overemphasized to the neglect of other factors that fed the recent financial
collapse, from "interest rates that were kept too low for too long" to
"failures of corporate governance." New regulations may be slowed

Signs are emerging that new regulations will be slowed, if not watered down
altogether. Canadian central bank governor Mark Carney warned in a mid-June
speech that "we should not sacrifice our ambition for these measures to
speed of implementation, nor the economic recovery to an arbitrary
timeline." But the G-20's ambitions have already been enormously scaled back
since the group's first major summit on financial regulation in Washington
in 2008.

"There was all this enthusiasm; they were going to reorganize the
international financial system, the US wanted a global bank tax, some of the
European leaders were keen on getting rid of hedge funds," says Ivan Savic,
a political economist at the G-20 Research Group at the University of
Toronto. "That was just way too ambitious; this is a very heterogenous
group."

Dr. Savic says he's sympathetic for the need for balance in regulation, but
warns that time is growing short. "The trick with financial regulation in
responding to a crisis is, if you react too heavy-handedly too early, you
can ... hurt the recovery," he says. "But the longer you wait for the
recovery, the stronger financial markets get and they say 'we'll fight you
on this.' Look at Wall Street: It was at first very contrite and now, I
think we see them flexing their muscles again."