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Mike Chelen

Qualifying Online Information Resources for Chemists | SciVee - 0 views

shared by Mike Chelen on 11 Dec 08 - Cached
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    his meeting was about "Making the Web Work for Science and the Impact of e-Science and the Cyberinfrastructure." I provided an overview of how access to information has changed over the past 20 years for me. I talked about the challenges for publishers serving the chemistry community and how their business models are being challenged and how I empathize with the struggle to figure out how to deal with it. I talked about quality and how care must be taken when using information online. We are ALL challenged with errors - whether you consider PubChem, ChemSpider, Wikipedia or any of the other online databases they all have errors - how do you find them? Some of them are obvious and I pointed to obvious examples in the talk. I hoped to educate the attendees in regards to the value of InChI which, while not a perfect fit yet, is a great start to structure-based communication of chemistry. I publicly blessed the efforts of publishers such as the RSC and Nature Publishing group for the efforts they are making to support InChI and improve the quality of document presentation online. I blessed CAS as a treasure trove of information and the gold standard of curated chemistry. We need them all to be successful for the sake of our science. The challenge is how to fit into the ongoing proliferation of free access to information without modifying the business models.
seth kutcher

Remote Computer Assistance - 1 views

My computer often experiences trouble and I could hardly find someone to fix it for me, especially when it happens during the wee hours of the morning. My friend told me about Computer Assistance O...

computer assistance

started by seth kutcher on 08 Nov 11 no follow-up yet
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.
Mike Chelen

Peter Suber, Open Access News - 0 views

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    Law professors defend NIH policy against copyright objections Forty-six law professors and specialists in copyright law wrote to the House Judiciary Committee on September 8 to show that the publishing lobby's objections to the NIH policy misrepresent US copyright law. The Committee had the letter in hand when it convened the September 11 hearing on the Conyers bill. The letter is now online. Excerpt:
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

SourceForge.net: Kaltura - video for any site, wiki, blog - 0 views

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    Kaltura's open-source online video platform for video management, creation, remix and collaboration. Download our MediaWiki video extension and WordPress plugin and contribute for more. Be part of the community at http://community.kaltura.org
Mike Chelen

ChemSpider - Database of Chemical Structures and Property Predictions - 0 views

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    ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services ChemSpider is the richest single source of structure-based chemistry information.
dev j

Online editing services - 0 views

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    Welcome to Manuscriptedit.com, your online partner for English language editing, proofreading, medical writing, formatting, design & development and publication support services. We offer a comprehensive manuscript editing service before its submission for publication as well as after acceptance by the peer review process.
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

Main Page - GenBioWiki - 0 views

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    GenBioWiki is the student home page for the Genetics, Bioinformatics, and Computational Biology (GBCB) program at Virginia Tech. Bioinformatics and computational biology provide a research platform to acquire, manage, analyze, and display large amounts of data, which in turn catalyze a systems approach to understanding biological organisms, as well as making useful predictions about their behavior in response to environmental and other perturbations. Moreover, bioinformatics is the study of biological systems and large biological data sets using analytical methods borrowed from computer science, mathematics, statistics, and the physical sciences. This transdisciplinary approach to research requires graduates with extensive cross-cultural professional and technical training and provides ample employment opportunities for Ph.D. graduates. [1]
Mike Chelen

Protocol for Implementing Open Access Data - 0 views

  • information for the Internet community
  • distributing data or databases
  • “open” and “open access”
  • ...69 more annotations...
  • 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
  • copyright
  • 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
  • copyright begins in and ends in many databases
  • 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
  • copyright in situations where it is not necessary
  • 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
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