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Open Source - History and Development | Walker | Open and Libraries Class Journal

Thu, 17 Mar 2011 19:55:41 -0000

Tags: opensource_technology, history, automotive, Ford, Selden

by: Sam Rose

Creative Commons Attribution Noncommercial ShareAlike Legal Code

Fri, 22 May 2009 13:11:11 -0000

Highlights and Sticky Notes:

must include a copy of, or the Uniform Resource Identifier for, this License with every copy

Derivative Work

the terms of this License

distribute

may not exercise

rights granted to You in Section 3 above

primarily intended for or directed toward commercial advantage or private monetary compensation

primarily

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

name of the Original Author

keep intact all copyright notices for the Work

"Attribution Parties"

Tags: no_tag

by: Mike Chelen

Science 2.0 – introduction and perspectives for Poland « Freelancing science

Wed, 20 May 2009 01:30:13 -0000

Highlights and Sticky Notes:

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

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

least radical idea you can find in modern Science 2.0 world

virtual research environment

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.

participation in online communities

important part of Science 2.0 is the fact that it has human face

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

synthetic biology

not all universities in world have synthetic biology courses

didn’t stop these students, and they plan to participate in IGEM again

not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry

community of life scientists

even people without direct connection to science

diverse skills and background

online conference

interact with them and to learn from them

Tags: science2.0, elearning, eresearch

by: Mike Chelen

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

Fri, 15 May 2009 10:59:29 -0000

Highlights and Sticky Notes:

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

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

make it easy for researchers to deliver on their obligations

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”

don’t tend to be concerned about freeloading

providing clear guidance and tools

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

Tags: open, public, science, data, license

by: Mike Chelen

Open Science and Information

Fri, 01 May 2009 08:32:45 -0000

Comments:

semantic mediawiki for testing and development - Mike Chelen

Tags: opensci, mediawiki, semantic

by: Mike Chelen

VOS: Virtuoso Open-Source Edition

Thu, 23 Apr 2009 11:20:51 -0000

Tags: vituoso, opensource, rdf

by: Mike Chelen

Edge of Space Found | LiveScience

Fri, 10 Apr 2009 07:56:32 -0000

Highlights and Sticky Notes:

boundary between Earth's atmosphere and outer space

instrument developed by scientists at the University of Calgary

73 miles (118 kilometers) above Earth's surface

astronauts can say they've been to space after only passing the 50-mile (80-kilometer) mark

space industry is also a somewhat arbitrary 62 miles (100 kilometers)

United States, however, has never officially adopted a set boundary standard

overflight rights of satellites and other orbiting bodies

NASA's mission control uses 76 miles (122 kilometers) as their re-entry altitude

shuttle switches from steering with thrusters to maneuvering with air surfaces

13 million miles (21 million kilometers)

the boundary where Earth's gravity is no longer dominant

Supra-Thermal Ion Imager

tracking the relatively gentle winds of Earth's atmosphere and the more violent flows of charged particles in space

difficult to make measurements in this region, which is too high for balloons and too low for satellites

second time that direct measurements of charged particle flows have been made in this region

first time all the ingredients – such as the upper atmospheric winds – have been included

David Knudsen of the University of Calgary

carried by the JOULE-II rocket on Jan. 19, 2007

an altitude of about 124 miles (200 kilometers) above sea level and collected data for the five minutes it was moving through the "edge of space."

Journal of Geophysical Research on April 7

space weather and its impacts on Earth

calculate energy flows into the Earth's atmosphere that ultimately may be able to help us understand the interaction between space and our environment

link between sunspots and the warming and cooling of the Earth's climate

how space weather impacts satellites, communications, navigation, and power systems

Tags: space, solar_wind

by: Mike Chelen

Using the Google Plugin for Eclipse - Google App Engine - Google Code

Wed, 08 Apr 2009 15:14:05 -0000

Highlights and Sticky Notes:

Eclipse 3.4 (Ganymede)

Help menu > Software Updates...

Guestbook

http://dl.google.com/eclipse/plugin/3.4

Google Plugin for Eclipse 3.4

Google Web Toolkit SDK

Google App Engine Java SDK

Install...

restart

File menu > New > Web Application Project

Add Site...

Project name

Package

guestbook

Verify that "Use Google App Engine" is checked.

Finish

Run menu, Debug As > Web Application

App Engine deploy button uploads your application to App Engine:

edit the appengine-web.xml file and change the <application>...</application> element to contain the new ID

administrator account username (your email address) and password

Tags: google, appengine, java, eclipse, plugin

by: Mike Chelen

EclipsePlugin - GitWiki

Fri, 06 Mar 2009 03:32:32 -0000

Highlights and Sticky Notes:

Point the update manager to http://www.jgit.org/update-site and install.

Tags: git, eclipse

by: Mike Chelen

Main Page - Open Bioinformatics Foundation

Mon, 22 Sep 2008 13:00:27 -0000

Comments:

The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.

The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects.

Our main activities are:

* Underwriting and supporting the BOSC conferences
* Organizing and supporting developer-centric "hackathon" events
* Managing our servers, colocation facilities, bank account & other assets

We are incorporated in the state of Delaware, USA as a not-for-profit company. - Mike Chelen

Tags: open, biology, informatics

by: Mike Chelen

Home :::Academic Journals

Sun, 01 Mar 2009 06:32:40 -0000

Comments:

ACADEMIC JOURNALS provides free access to research information to the international community without financial, legal or technical barriers. All the journals from this organization will be freely distributed and available from multiple websites.....ACADEMIC JOURNALS, breaking new frontiers in the world of journals. - Mike Chelen

Tags: journals, academic, open, access, article, science, research

by: Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Comments on the Science Commons Protocol for Implementing Open Access Data

Sun, 01 Mar 2009 02:03:52 -0000

Highlights and Sticky Notes:

the protocol does not discuss any of the possible attractions of allowing such provisions

Protocol gives 3 basic reasons for preferring the ‘PD’ approach

Science Commons Protocol for Implementing Open Access Data

I am not really convinced by any of these points that attribution or share-alike provisions should not be included in open data licenses

application of obligations based on copyright in situations where it is not necessary

non-copyrightable elements extends to the entire database and inadvertently infringe

If intellectual property rights are involved

requirements carrying a stiff penalty for failure

selective waiving of intellectual property rights

interpretative problems

Tags: open, access, data, okfn, science, commons

by: Mike Chelen

Protocol for Implementing Open Access Data

Sun, 07 Sep 2008 22:47:24 -0000

Highlights and Sticky Notes:

information for the Internet community

distributing data or databases

“open” and “open access”

requirements for gaining and using the Science Commons Open Access Data Mark and metadata

interoperability of scientific data

terms and conditions around data make integration difficult to legally perform

single license

data with this license can be integrated with any other data under this license

too many databases under too many terms already

unlikely that any one license or suite of licenses will have the correct mix of terms

principles for open access data and a protocol for implementing those principles

Open Access Data Mark and metadata

databases and data

the foundation to legally integrate a database or data product

another database or data product

no mechanisms to manage transfer or negotiations of rights unrelated to integration

submitted to Science Commons for certification as a conforming implementation

Open Access Data trademarks (icons and phrases) and metadata on databases

protocol must promote legal predictability and certainty

easy to use and understand

lowest possible transaction costs on users

Science Commons’ experience in distributing a database licensing Frequently Asked Questions (FAQ) file

hard to apply the distinction between what is copyrightable and what is not copyrightable

lack of simplicity restricts usage

reducing or eliminating the need to make the distinction between copyrightable and non-copyrightable elements

satisfy the norms and expectations of the disciplines providing the database

norms for citation will differ

norms must be attached

Converge on the public domain by waiving all rights based on intellectual property

reconstruction of the public domain

scientific norms to express the wishes of the data provider

public domain

waiving the relevant rights on data and asserting that the provider makes no claims on the data

Requesting behavior, such as citation, through norms rather than as a legal requirement based on copyright or contracts, allows for different scientific disciplines to develop different norms for citation.

waive all rights necessary for data extraction and re-use

sui generis database rights

claims of unfair competition

implied contracts

and other legal rights

any obligations on the user of the data or database such as “copyleft” or “share alike”, or even the legal requirement to provide attribution

non-legally binding set of citation norms

waiving other statutory or intellectual property rights

there are other rights, in addition to copyright, that may apply

uncopyrightable databases may be protected in some countries

sui generis rights apply in the European Union

waivers of sui generis and other legal grounds for database protection

no contractual controls

using contract, rather than intellectual property or statutory rights, to apply terms to databases

affirmatively declare that contractual constraints do not apply to the database

interoperation with databases and data not available under the Science Commons Open Access Data Protocol through metadata

data that is not or cannot be made available under this protocol

owner provides metadata (as data) under this protocol so that the existence of the non-open access data is discoverable

digital identifiers and metadata describing non-open access data

“Licensing” a database typically means that the “copyrightable elements” of a database are made available under a copyright license

Database FAQ, in its first iteration, recommended this method

recommendation is now withdrawn

database divided into copyrightable and non copyrightable elements

user tends to assume that all is under copyright or none is under copyright

share-alike license on the copyrightable elements may be falsely assumed to operate on the factual contents of a database

query across tens of thousands of data records across the web might return a result which itself populates a new database

selective waiving of intellectual property rights fail to provide a high degree of legal certainty and ease of use

problem of false expectations

apply a “copyleft” term to the copyrightable elements of a database, in hopes that those elements result in additional open access database elements coming online

uncopyrightable factual content

republish those contents without observing the copyleft or share-alike terms

cascading attribution if attribution is required as part of a license approach

Would a scientist need to attribute 40,000 data depositors in the event of a query across 40,000 data sets?

conflict with accepted norms in some disciplines

imposes a significant transaction cost

Tags: science, commons, open, access, data, public, domain

by: Mike Chelen

OAI Repository Explorer

Fri, 20 Feb 2009 06:31:38 -0000

Tags: oai, open, archive, web, repository

by: Mike Chelen

The Control Fallacy: Why OA Out-Innovates the Alternative : Nature Precedings

Wed, 11 Feb 2009 04:18:27 -0000

Comments:

This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of “end to end” network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers. - Mike Chelen

Tags: open, science, data, license

by: Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Open Data: Openness and Licensing

Wed, 11 Feb 2009 04:04:21 -0000

Comments:

Why bother about openness and licensing for data? After all they don’t matter in themselves: what we really care about are things like the progress of human knowledge or the freedom to understand and share. - Mike Chelen

Highlights and Sticky Notes:

Why bother about openness and licensing for data

It’s crucial because open data is so much easier to break-up and recombine, to use and reuse.

want people to have incentives to make their data open and for open data to be easily usable and reusable

good definition of openness acts as a standard that ensures different open datasets are ‘interoperable’

Licensing is important because it reduces uncertainty. Without a license you don’t know where you, as a user, stand: when are you allowed to use this data? Are you allowed to give to others? To distribute your own changes, etc?

licensing and definitions are important even though they are only a small part of the overall picture

If we get them wrong they will keep on getting in the way of everything else.

Everyone agrees that requiring attribution is OK

My opinion is that there should be no requirements, including attribution, and that standards should be community-based instead of legal. - Mike Chelen

Even if a basic license is used it can be argued that any ‘requirements’ for attribution or share-alike should not be in a license but in ‘community norms’.

Licenses and community norms are not exclusive. It's recommended to adopt a Public Domain license, and encourage attribution through community standards. - Mike Chelen

A license is likely to elicit at least as much, and almost certainly more, conformity with its provisions than community norms.

Ease of access and should be the goal, not conformity. - Mike Chelen

(even to a user it is easy to comply with the open license)

It is important to specifically publish using a Public Domain dedication. - Mike Chelen

Tags: okfn, blog, open, data, science, license

by: Mike Chelen

Main Page - OpenResearch.org

Fri, 06 Feb 2009 08:37:27 -0000

Comments:

This semantic wiki at OpenResearch.org aims at making the world of science more visible and accessible. Everybody can add his favorite events (e.g. conferences and workshops), co-workers, tools / datasets, community fora or journals. Pooled together these pieces of information constitute a vast knowledge base about who and what moves science forward. - Mike Chelen

Tags: semantic, wiki, open, research, science

by: Mike Chelen

SourceForge.net: Staden Package

Wed, 04 Feb 2009 05:53:16 -0000

Comments:

A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. - Mike Chelen

Tags: dna, open, source, gap4, spin

by: Mike Chelen

Portal:Gene Wiki - Wikipedia, the free encyclopedia

Thu, 29 Jan 2009 09:58:26 -0000

Comments:

Welcome to the Gene Wiki portal. This portal is dedicated to the goal of applying community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows:

* To provide a well written and informative Wikipedia article for every notable human gene
* To invite participation by interested lay editors, students, professionals, and academics from around the world
* To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both

Please browse around the Gene Wiki, make an edit to your favorite gene page, and feel free to ask questions! - Mike Chelen

Tags: genetics, wiki, wikipedia, gene, science, biology

by: Mike Chelen

Wikipedia:WikiProject NIH - Wikipedia, the free encyclopedia

Thu, 29 Jan 2009 09:06:54 -0000

Comments:

Welcome to the NIH WikiProject, a collaboration area and group of editors dedicated to improving Wikipedia's coverage of National Institutes of Health. This is a new WikiProject, so please join!!

(For more information on WikiProjects, please see Wikipedia:WikiProject and the Guide to WikiProjects).

Goals

* Improve Wikipedia's current coverage of the NIH and deepen the coverage with more pages.

Scope

* Cover all of the Institutes all the way down to individual laboratories/units.

- Mike Chelen

Tags: wiki, nih, research, science, wikipedia

by: Mike Chelen