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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
  • ...44 more annotations...
  • 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

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
  • ...8 more annotations...
  • 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.
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    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

#955 (importing magnet links) - The libTorrent and rTorrent Project - Trac - 0 views

  • 08/31/08 12:55:48 changed by josef ¶ I've written a patch to support magnet links now. You need to check out svn rev 1065 of libtorrent/rtorrent, and get http://ovh.ttdpatch.net/~jdrexler/rt/experimental/dht-pex-static_map.diff and http://ovh.ttdpatch.net/~jdrexler/rt/experimental/magnet-uri.diff then in the directory that has the libtorrent and rtorrent subdirs you've checked out, do patch -p0 < dht-pex-static_map.diff patch -p0 < magnet-uri.diff and recompile both. It uses the official magnet protocol from Bittorrent BEP-0009 which is incompatible with Azureus and so far only supported by uTorrent 1.8+, so it'll only work if there are recent uTorrents in the swarm. It supports magnet links in both the old style base32 encoded hashes as well as the recommended URL-encoded hashes. Note that if there is one or more tracker URLs to use for the download, it must be present as "tr=..." argument in the magnet URI, because there is currently no way of adding trackers in rtorrent afterwards, so without that it'll use DHT and nothing else. After opening a magnet URI, it will add a meta download to download the actual torrent info. When that is complete, it is replaced by the real torrent. The meta data is saved in your standard torrent download directory, you can delete that after the real torrent has appeared, or you can keep it in case you need to open the same magnet URI again.
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    Importing magnet links would be great, because some sites only have magnet links. Mayby something like this:
Mike Chelen

BMC Biology - 0 views

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    BMC Biology - the flagship biology journal of the BMC series - publishes research and methodology articles of special importance and broad interest in any area of biology and biomedical sciences. BMC Biology (ISSN 1741-7007) is covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.
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.
Mike Chelen

OPENCV \ library - 0 views

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    OpenCV is an open source computer vision library originally developed by Intel. It is free for commercial and research use under a BSD license. The library is cross-platform, and runs on Mac OS X, Windows and Linux. It focuses mainly towards real-time image processing, as such, if it finds Intel's Integrated Performance Primitives on the system, it will use these commercial optimized routines to accelerate itself. This implementation is not a complete port of OpenCV. Currently, this library supports : * real-time capture * video file import * basic image treatment (brightness, contrast, threshold, …) * object detection (face, body, …) * blob detection Future versions will include more advanced functions such as motion analysis, object and color tracking, multiple OpenCV object instances … For more information about OpenCV visit the Open Source Computer Vision Library Intel webpage, the OpenCV Library Wiki, and the OpenCV Reference Manual (pdf).
Mike Chelen

Qualifying Online Information Resources for Chemists - SlideShare - 0 views

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    The presentation provides an overview of some of the challenges the publishers face moving forward, how they are responding to it, how InChI is an enabling technology, how quality is important.
Mike Chelen

Bjoern Hassler - The Science Media Network: Mediawiki OER export - 0 views

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    In the page on Thoughs on institutional OER contributions I argue that (among other things) having a good export of material from shared resources (like the OER Toolkit or wikieducator) is important for getting institutions to contribute. How is this requirement met by the platform used for the OER Toolkit and wikieducator?
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

SWAN (Semantic Web Applications in Neuromedicine) Project - 0 views

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    SWAN (Semantic Web Applications in Neuromedicine) is a Web-based collaborative program that aims to organize and annotate scientific knowledge about Alzheimer disease (AD) and other neurodegenerative disorders. Its goal is to facilitate the formation, development and testing of hypotheses about the disease. The ultimate goal of this project is to create tools and resources to manage the evolving universe of data and information about AD in such a way that researchers can easily comprehend their larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease. The SWAN project is designed to allow the community of AD researchers to author, curate and connect a diversity of data and ideas about AD via secure personal and public SWAN workspaces, using the emerging Semantic Web paradigm for deep interconnection of data, information and knowledge. We are initially focusing on developing a fully public Web resource deployed as part of the Alzheimer Research Forum web site (www.alzforum.org). After the public resource has been launched, we will also develop secure personal workspaces (MySWAN) and semi-private lab workspaces (LabSWAN). An essential component of this project is development of an initial, core knowledge base within SWAN, which will provide immediate value to researchers at the time of deployment. This is a critically important part of our strategy to ensure that the SWAN system gains wide adoption and active participation by the AD research community. As part of our development strategy, we are also recruiting a "beta test" community of AD researchers to enter their own hypotheses, add commentaries and citations, and provide feedback on the technology and content. SWAN is being developed by a collaborative team from
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