Mike Chelen's Public Library

13 Nov 09

SSH and ssh-agent

www.securityfocus.com/...1812 - Preview

ssh -o'RSAAuthentication=no' -o 'PubkeyAuthentication=no' user@myserver

05 Nov 09

Raiden's Realm: Tutorial: Start screen and automatically run a command

www.raiden.net/...and_automatically_run_acommand - Preview

screen -d -m -S LinuxMint btdownloadheadless.py mint.torrent

30 Oct 09

Economics focus: E pluribus tunum | The Economist

www.economist.com/...displaystory.cfm - Preview

bought something for less than they were willing to pay
difference between the price paid and the most a buyer would have agreed to
33 more annotations...
- consumer surplus
- the part of the overall economic benefit from any trade that the buyer gets
- rest of the surplus from a trade goes to the seller
- merchant wants to sell to each customer at a price as close as possible to the most that client would be willing to pay
- this is impossible if everyone is charged the same price
- tailor prices to people’s willingness to pay or price-sensitivity
- vendors in street markets do when they offer naive tourists a higher price than seasoned locals
- sellers can still encourage people to sort themselves into groups which can be charged different prices
- Those who are particularly keen to get their hands on a copy of a new book, for instance, may be willing to pay a higher price for it
- These tactics and others, like selling things in bundles rather than individually, all exploit differences in people’s sensitivity to price.
- sellers and buyers would act under different pricing schemes
- information about how those who buy music online value different songs
- 500 undergraduate students at Wharton
- 50 most popular songs on iTunes earlier that month
  - is this representative of the entire library? - on 2009-10-30
  Add Sticky Note
- Similar data were also collected in January this year, though this time some older and less popular tracks were also included
- uniform price per song that maximised revenue among the students
- $2.30 in 2008 and $1.46 in 2009
- Wharton students may be particularly fond of music
  - age group may also be relatively fond of digital music, and socioeconomic class could have higher spending habits than average - on 2009-10-30
  Add Sticky Note
- song-specific pricing
- increase profits by a mere 3%
- people who valued one song highly also tended to place a high value on others
- person-specific, rather than song-specific, pricing would be more efficient
- sellers’ data are not refined enough to set different prices for different people
- basic demographic information did not tell them much about musical tastes
- according to the 2009 survey data, would be generated by charging the students $21.19 for entry and 37 cents a song
- raise the producer surplus by 30%
- Consumer surplus would also rise in this instance
- buy songs they would have not have done at a higher uniform price
- Spotify
- monthly fee for songs without limit
- several songs together in a bundle (much like an album)
- For example, charging $16.95 for all 50 songs studied (which would have cost $49.50 to download) would leave profit unchanged because enough people would buy.
- it would increase consumer surplus by around 50% by attracting new buyers

27 Oct 09

BBC NEWS | Technology | Government opens data to public

news.bbc.co.uk/...8311627.stm - Preview

"I would like to suggest: sure, make a beautiful website, but first, give us - all of us - the unadulterated data. We have to ask for raw data now."

16 Oct 09

Is there a way to batch recalculate all nodes? | drupal.org

drupal.org/195013 - Preview

Views Bulk Operations
node_save($object);

14 Oct 09

Slicehost Forum - ssh-add error: Could not open a connection to your authentication agent.

forum.slicehost.com/comments.php - Preview

exec ssh-agent bash

13 Oct 09

Howto: Use rtorrent like a pro « Motho ke motho ka botho

kmandla.wordpress.com/...howto-use-rtorrent-like-a-pro - Preview

screen rtorrent
press Ctrl-a d and it will detach
1 more annotations...
- screen -r

08 Oct 09

How To Specify A Custom php.ini For A Web Site (Apache2 With mod_php) | HowtoForge - Linux Howtos and Tutorials

www.howtoforge.com/a-website-apache2-with-mod_php - Preview

/etc/php5/apache2/php.ini

07 Oct 09

SQL Databases Don't Scale

adamblog.heroku.com/...sql_databases_dont_scale - Preview

MySQL’s killer feature is easy configuration of master-slave replication, where you have a read-only slave database that replicates everything coming to the master database in realtime.
sends any reads (SELECT) to one of the read slaves, while only sending writes (INSERT, UPDATE, DELETE) to the master
6 more annotations...
- horizontal scaling on the read side
- The read slave technique is the best option for scaling SQL databases.
- transparent to the application
- master server is a bottleneck
- write-heavy applications
- single point of failure

18 Jun 09

Generate SVG from XMLwith XSLT: Example

surguy.net/...simpleinline.xml - Preview

xml svg xslt xhtml

25 May 09

Data scraping with YQL and jQuery | kelvinluck.com

www.kelvinluck.com/...a-scraping-with-yql-and-jquery - Preview

jquery yql yahoo

need a list of all the US National Parks in XML format
grab the data from this list on Wikipedia
10 more annotations...
- navigating a HTML DOM
- jQuery to parse the data
- XPath to your YQL
- relevant table from the Wikipedia document
- SELECT * FROM html WHERE url="http://en.wikipedia.org/wiki/List_of_United_States_National_Parks_by_state" AND xpath="//table[@class='wikitable sortable']"
- XML or JSON
- creating an XML document
- AJAX call from jQuery and then loop over the JSON
- CSS style selection engine as well as the XPath one
  - added recently- http://developer.yahoo.net/blog/archives/2009/04/yql_execute.html - on 2009-05-25
  Add Sticky Note
- documentation could maybe be clearer

24 May 09

Yahoo! Query Language - YDN

developer.yahoo.com/console - Preview

yahoo yql developer console

XML Path Language (XPath)

www.w3.org/xpath - Preview

xpath

ancestor::div selects all div
ancestors of the context node

22 May 09

Creative Commons Attribution Noncommercial ShareAlike Legal Code

creativecommons.org/...legalcode - Preview

must include a
copy of, or the Uniform Resource Identifier for, this
License with every copy
Derivative Work
11 more annotations...
- the terms of this License
- distribute
- rights granted to You
  in Section 3 above
- primarily
- primarily
  intended for or directed toward commercial advantage or
  private monetary compensation
- may not exercise
- exchange of the Work
  for other copyrighted works by means of digital
  file-sharing or otherwise shall not be considered to be
  intended for or directed toward commercial advantage or
  private monetary compensation
- provided there is no
  payment of any monetary compensation in connection with
  the exchange of copyrighted works
- keep intact all
  copyright notices for the Work
- name of
  the Original Author
- "Attribution Parties"

20 May 09

Science 2.0 – introduction and perspectives for Poland « Freelancing science

freelancingscience.com/...on-and-perspectives-for-poland - Preview

science2.0 elearning eresearch

transcript of Science 2.0 based on a presentation I gave on conference on open science organized in Warsaw earlier this month
prepared for mixed audience and focused on perspectives for Poland
45 more annotations...
- new forms of communication between scientists
- research become meaningful only after confronting results with the scientific community
- peer-reviewed publication is the best communication channel we had so far
- new communication channels complement peer-reviewed publication
- two important attributes in which they differ from traditional models: openness and communication time
- increased openness and shorter communication time happens already in publishing industry (via Open Access movement and experiments with alternative/shorter ways of peer-review)
- say few words about experiments that go little or quite a lot beyond publication
- My Experiment as an example of an important step towards openness
- virtual research environment
- least radical idea you can find in modern Science 2.0 world
- focus is put on sharing scientific workflows
- use case
- diagram of the “methods” sections from experimental (including bioinformatics analyses) publications
- make it easier for others to understand what we did
- can open towards other scientists we can also open towards non-experts
- people from all over the world compete in improving structural models of proteins
- helps in improving protein structure prediction software and in understanding protein folding
- combine teaching and data annotation
- metagenome sequences in first case and chemistry spectra in the second
- interactive visualizations of chemical structures, genomes, proteins or multidimensional data
- communicate some difficult concepts faster
- new approaches in conference reporting
- report in real time from the conference
- followed by a number of people, including even the ones that were already on the conference
- “open notebook science” which means conducting research using publicly available, immediately updated laboratory notebook
- The reason I did a model for Cameron’s grant was that I subscribed to his feed before
- I didn’t subscribe to Cameron because I knew his professional profile
- I read his blog, I commented on it and he commented on mine, etc.
- important part of Science 2.0 is the fact that it has human face
- participation in online communities
- PhDs about the same time
- first was from a major Polish institute, the second from a major European one
- what a head of a lab both would apply to will see
- gap we must fill, this is between current research and lectures we give today
- access to real-time scientific conversation
- follow current research and decide what is important to learn
- not all universities in world have synthetic biology courses
- synthetic biology
- didn’t stop these students, and they plan to participate in IGEM again
- community of life scientists
- not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry
- even people without direct connection to science
- diverse skills and background
- interact with them and to learn from them
- online conference

15 May 09

Science in the open » A breakthrough on data licensing for public science?

blog.openwetware.org/...a-licensing-for-public-science - Preview

open public science data license

Peter Murray-Rust and others at the Unilever Centre for Molecular Informatics at Cambridge
conversation we had over lunch with Peter, Jim Downing, Nico Adams, Nick Day and Rufus Pollock
28 more annotations...
- appropriate way to license published scientific data
- value of share-alike or copyleft provisions of GPL and similar licenses
- spreading the message and use of Open Content
- prevent “freeloaders” from being able to use Open material and not contribute back to the open community
- presumption in this view is that a license is a good, or at least acceptable, way of achieving both these goals
- allow people the freedom to address their concerns through copyleft approaches
- Rufus
- concerned more centrally with enabling re-use and re-purposing of data as far as is possible
- don’t tend to be concerned about freeloading
- worried by the potential for licensing to make it harder to re-use and re-mix disparate sets of data and content into new digital objects
- “license”, will have scientists running screaming in the opposite direction
- we focused on what we could agree on
- common position statement
- area of best practice for the publication of data that arises from public science
- there is a window of opportunity to influence funder positions
- data sharing policies
- “following best practice”
- providing clear guidance and tools
- make it easy for researchers to deliver on their obligations
- if it is widely accepted by their research communities
- “best practice is X”
- enable re-use and re-purposing of that data
- share-alike approaches as a community expectation
- Explicit statements of the status of data are required and we need effective technical and legal infrastructure to make this easy for researchers.
- “Where a decision has been taken to publish data deriving from public science research, best practice to enable the re-use and re-purposing of that data, is to place it explicitly in the public domain via {one of a small set of protocols e.g. cc0 or PDDL}.”
- focuses purely on what should be done once a decision to publish has been made
- data generated by public science
- describing this as best practice it also allows deviations that may, for whatever reason, be justified by specific people in specific circumstances

RNA world easier to make : Nature News

www.nature.com/...news.2009.471.html - Preview

rna

John Sutherland and his colleagues from the University of Manchester, UK
ribonucleotide
30 more annotations...
- building block of RNA
- 'RNA world' hypothesis, which suggests that life began when RNA, a polymer related to DNA that can duplicate itself and catalyse reactions
- strong evidence for the RNA world
- Donna Blackmond, a chemist at Imperial College London.
- RNA polymer is a string of ribonucleotides
- three distinct parts: a ribose sugar, a phosphate group and a base
- chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide
- efforts to connect ribose and base together have met with frustrating failure
- researchers have now managed to synthesise
- remedy is to avoid producing separate ribose-sugar and base subunits
- ribonucleotides
- makes a molecule whose scaffolding contains a bond that will
- be the key ribose-base connection
- atoms are then added around this skeleton
- final connection is to add a phosphate group
- influences the entire synthesis
- acting as a catalyst, it guides small organic molecules into making the right connections
- What we have ended up with is molecular choreography
- objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry
- flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth
- Robert Shapiro, a chemist at New York University
- early-Earth scenarios
- heating molecules in water, evaporating them and irradiating them with ultraviolet light
- results showing that they can string nucleotides together
- ultimate goal is to get a living system (RNA) emerging from a one-pot experiment
- need to know what the constraints on the conditions are first
- Shapiro sides with
- another theory of life's origins
- because RNA is too complex to emerge from small molecules, simpler metabolic processes
- eventually catalysed the formation of RNA and DNA

untitled - Twiddla.com

www.twiddla.com/101467 - Preview

Nice set of features, doesn't require flash, supports latex for equations, allows multiple snapshot save points. Export is limited to image (.png). - amiigo on 2009-05-15

13 May 09

WSJ Staff Not Allowed To Mix "Business And Pleasure" On Twitter (NWS)

www.businessinsider.com/and-pleasure-on-twitter-2009-5 - Preview

"discuss articles that haven't been published, meetings you've attended or plan to attend with staff or sources, or interviews that you've conducted."
- Reasonable for some cases, yet surely it would be okay to discuss meetings and interviews with public figures? - on 2009-05-13
Add Sticky Note
whether on Dow Jones sites or in social-networking, e-mail, personal blogs, or other sites outside Dow Jones
- This covers nearly every form of digital communication, and is tantamount to including phone calls for web-generation. - on 2009-05-13
Add Sticky Note
13 more annotations...
- Never misrepresent yourself using a false name when you're acting on behalf of your Dow Jones publication or service.
  - Part of good professional ethics, does this not apply already to all forms of communication? - on 2009-05-13
  Add Sticky Note
- Base all comments posted in your role as a Dow Jones employee in the facts, drawing from and citing your reporting when appropriate.
  - Good practice for all writers, and a reasonable goal in professional capacity. - on 2009-05-13
  Add Sticky Note
- Base all comments posted in your role as a Dow Jones employee in the facts, drawing from and citing your reporting when appropriate. Sharing your personal opinions, as well as expressing partisan political views, whether on Dow Jones sites or on the larger Web, could open us to criticism that we have biases and could make a reporter ineligible to cover topics in the future for Dow Jones.
- whether on Dow Jones sites or on the larger Web
  - Views expressed outside professional capacity should not be subject to approval by one's employer. - on 2009-05-13
  Add Sticky Note
- could open us to criticism that we have biases
  - Critical perspectives can be welcomed by unbiased authors to substantiate the claim their article is based on fact. - on 2009-05-13
  Add Sticky Note
- Consult your editor before "connecting" to or "friending" any reporting contacts who may need to be treated as confidential sources. Openly "friending" sources is akin to publicly publishing your Rolodex.
  - Very good technical advice, which some users may not be aware of. - on 2009-05-13
  Add Sticky Note
- Let our coverage speak for itself, and don't detail how an article was reported, written or edited.
  - These are not mutually exclusive, in that providing additional details can be valuable, if done to further an article that is already strong enough to stand on its own. - on 2009-05-13
  Add Sticky Note
- Don't discuss articles that haven't been published, meetings you've attended or plan to attend with staff or sources, or interviews that you've conducted.
  - Overly vague, what about discussing every day meetings with other staff? Encouraging employees to talk an editor in sensitive cases would be certainly be advisable however. - on 2009-05-13
  Add Sticky Note
- Don't disparage the work of colleagues or competitors or aggressively promote your coverage.
  - Goes back to #2, in that crticism is useful to the degree it is based on research and factual reporting. - on 2009-05-13
  Add Sticky Note
- Don't engage in any impolite dialogue with those who may challenge your work -- no matter how rude or provocative they may seem.
  - Great media/social media advice, agreed on by popular bloggers. - on 2009-05-13
  Add Sticky Note
- Avoid giving highly-tailored, specific advice to any individual on Dow Jones sites. Phrases such as "Travel agents are saying the best deals are X and Y..." are acceptable while counseling a reader "You should choose X..." is not. Giving generalized advice is the best approach.
  - The first phrase is indeed better, the reason is actually because it is *more* specific by providing evidence for its claim. - on 2009-05-13
  Add Sticky Note
- Common sense should prevail, but if you are in doubt about the appropriateness of a Tweet or posting, discuss it with your editor before sending.
  - Educated decision making and judgment of the professional remain the surest guarantee of high quality journalism. - on 2009-05-13
  Add Sticky Note
- Business and pleasure should not be mixed on services like Twitter.

01 May 09

Open Science and Information

semantic mediawiki for testing and development

opensciinfo.referata.com/...Main_Page - Preview

opensci mediawiki semantic

Mike Chelen's Public Library

SSH and ssh-agent

Raiden's Realm: Tutorial: Start screen and automatically run a command

Economics focus: E pluribus tunum | The Economist

BBC NEWS | Technology | Government opens data to public

Is there a way to batch recalculate all nodes? | drupal.org

Slicehost Forum - ssh-add error: Could not open a connection to your authentication agent.

Howto: Use rtorrent like a pro « Motho ke motho ka botho

How To Specify A Custom php.ini For A Web Site (Apache2 With mod_php) | HowtoForge - Linux Howtos and Tutorials

SQL Databases Don't Scale

Generate SVG from XMLwith XSLT: Example

Data scraping with YQL and jQuery | kelvinluck.com

Yahoo! Query Language - YDN

XML Path Language (XPath)

Creative Commons Attribution Noncommercial ShareAlike Legal Code

Science 2.0 – introduction and perspectives for Poland « Freelancing science

Science in the open » A breakthrough on data licensing for public science?

RNA world easier to make : Nature News

untitled - Twiddla.com

WSJ Staff Not Allowed To Mix "Business And Pleasure" On Twitter (NWS)

Open Science and Information

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