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Contents contributed and discussions participated by Mike Chelen

Mike Chelen

Creative Commons Attribution Noncommercial ShareAlike Legal Code - 0 views

  • must include a copy of, or the Uniform Resource Identifier for, this License with every copy
  • Derivative Work
  • the terms of this License
  • ...10 more annotations...
  • 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"
Mike Chelen

Science 2.0 - introduction and perspectives for Poland « Freelancing science - 0 views

  • 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
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  • 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
Mike Chelen

Science in the open » A breakthrough on data licensing for public science? - 0 views

  • 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
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  • 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
Mike Chelen

Open Science and Information - 0 views

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    semantic mediawiki for testing and development
Mike Chelen

Edge of Space Found | LiveScience - 0 views

  • 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
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  • 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
Mike Chelen

Using the Google Plugin for Eclipse - Google App Engine - Google Code - 0 views

  • Eclipse 3.4 (Ganymede)
  • Help menu > Software Updates...
  • Guestbook
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  • 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:
  • register an application ID with App Engine using the Admin Console
  • 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
Mike Chelen

EclipsePlugin - GitWiki - 0 views

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

Home :::Academic Journals - 1 views

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    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

Open Knowledge Foundation Blog » Blog Archive » Comments on the Science Commo... - 0 views

  • 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
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  • 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
Mike Chelen

The Control Fallacy: Why OA Out-Innovates the Alternative : Nature Precedings - 0 views

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    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

Open Knowledge Foundation Blog » Blog Archive » Open Data: Openness and Licen... - 0 views

  • 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
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  • 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
    • Mike Chelen
       
      My opinion is that there should be no requirements, including attribution, and that standards should be community-based instead of legal.
  • 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’.
    • Mike Chelen
       
      Licenses and community norms are not exclusive. It's recommended to adopt a Public Domain license, and encourage attribution through community standards.
  • A license is likely to elicit at least as much, and almost certainly more, conformity with its provisions than community norms.
    • Mike Chelen
       
      Ease of access and should be the goal, not conformity.
  • (even to a user it is easy to comply with the open license)
    • Mike Chelen
       
      It is important to specifically publish using a Public Domain dedication.
  •  
    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

Main Page - OpenResearch.org - 0 views

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    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

SourceForge.net: Staden Package - 0 views

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

Portal:Gene Wiki - Wikipedia, the free encyclopedia - 0 views

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    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

Wikipedia:WikiProject NIH - Wikipedia, the free encyclopedia - 0 views

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    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

#opensciinfo - Twitter Search - 0 views

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    search for #opensciinfo hashtag used in twitter "room"
Mike Chelen

genome.gov | A Catalog of Published Genome-Wide Association Studies - 0 views

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    The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). SNP-trait associations listed here are limited to those with p-values < 1.0 x 10-5. Note that we are now including all identified SNP-trait associations meeting this p-value threshhold. Multipliers of powers of 10 in p-values are rounded to the nearest single digit; odds ratios and allele frequencies are rounded to two decimals. Standard errors are converted to 95 percent confidence intervals where applicable. Allele frequencies, p-values, and odds ratios derived from the largest sample size, typically a combined analysis (initial plus replication studies), are recorded below if reported; otherwise statistics from the initial study sample are recorded. Odds ratios < 1 in the original paper are converted to OR > 1 for the alternate allele. Where results from multiple genetic models are available, we prioritized effect sizes (OR's or beta-coefficients) as follows: 1) genotypic model, per-allele estimate; 2) genotypic model, heterozygote estimate, 3) allelic model, allelic estimate. Gene regions corresponding to SNPs were identified from the UCSC Genome Browser. Gene names are those reported by the authors in the original paper. Only one SNP within a gene or region of high linkage disequilibrium is recorded unless there was evidence of independent association.
Mike Chelen

EcoliHub - a comprehensive K-12 information resource - Home - 0 views

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    Sixty years of study have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its great importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub uses web services that are being developed to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life. Read More EcoliHub is being developed to serve the user community. Users can help teach us what is desirable in future releases by taking our User Survey.
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