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  2. April | 2007 | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/04/
    17 Jan 2022: By Open I mean that anyone can, in principle download, copy or clone part or all of the site, re-use … Continue reading.
  3. https://blogs.ch.cam.ac.uk/cosblog/author/rl201/feed/index.xml

    https://blogs.ch.cam.ac.uk/cosblog/author/rl201/feed/index.xml
    17 Jan 2022: video – the display pauses for a bit while the next bunch of data downloads and then the cute kittens start moving again. ... online video – the display pauses for a bit while the next bunch of data downloads and then the cute kittens start moving
  4. Content-mining: Using Tabula | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2013/11/26/content-mining-using-tabula/
    17 Jan 2022: And now you can download Tabula and run it on your own computer, like you would with OpenRefine. ... Note: You’ll need a copy of Java installed. You can download Java here.
  5. crystaleye | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/category/crystaleye/
    17 Jan 2022: These explain his thinking of why a series of medium-sized chunks is a better way to support the download of CrystalEye than one … Continue reading.
  6. Licensing Data | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/02/09/licensing-data/
    17 Jan 2022: research data through a data centre, repository or archive. ‘How to License Research Data’ is available for online reading or download.
  7. FoX marches on | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/12/22/fox-marches-on/
    17 Jan 2022: download from <>). This new release features. extended portability across compilers.
  8. Vote for Avogadro | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/06/24/vote-for-avogadro/
    17 Jan 2022: So. far, we’ve had over 40,000 downloads, been translated into 14. ... EVEN IF YOU ARE NOT A CHEMIST, WATCH THE VIDEO (SEE BELOW) AND IF YOU ARE COMPUTER-LITERATE DOWNLOAD AND PLAY WITH IT.
  9. OPSIN on Safari | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2010/11/23/opsin-on-safari/
    17 Jan 2022: I’m happy to anounce a new addition. The Safari Extension for Opsin (download) allows the user to highlight a chemical name in a web page and then control click affords
  10. Alpha and beta | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/04/25/alpha-and-beta/
    17 Jan 2022: Now ChemZoo is a commercial company, the data are not open (at least not explicitly – can anyone download the whole data base and if so what license covers it) and the ... In contrast Pubchem is open – anyone – like us can download the whole data.
  11. August | 2010 | petermr's blog | Page 2

    https://blogs.ch.cam.ac.uk/pmr/2010/08/page/2/
    17 Jan 2022: Now is your chance to Download documents robotically Run semantifiers over them Do natural language processing Extract data from raw text … Continue reading.
  12. What is a citation? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2006/12/09/what-is-a-citation/
    17 Jan 2022: From: BioMed Central Editorial. To: Peter Murray-Rust. Subject: Download statistics for your Open Access article. ... Total accesses to this article: 1143. Access figures include full text, abstract and PDF downloads from the BMC Bioinformatics website.
  13. ATOMic crystals | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/30/atomic-crystals/
    17 Jan 2022: remember when to download and what the size of chunk are.
  14. https://blogs.ch.cam.ac.uk/pmr/tag/fox/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/tag/fox/feed/index.xml
    17 Jan 2022: of version 3.1br / This is to announce the release of version 3.1 of the FoX library.br / (download from <a
  15. Panton Discussions online | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/02/02/panton-discussions-online/
    17 Jan 2022: We’ve already had a significant number of downloads. I think this is a useful format and I particularly appreciated the reverse (where Richard Grant interviewed my for F1000).
  16. What is strongOA? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/04/30/what-is-strongoa/
    17 Jan 2022: OA means that any user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article [PMR: without ... I believe is possible for anyone to download a complete journal,
  17. Is this paper Open Access? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2012/08/07/is-this-paper-open-access/
    17 Jan 2022: It is gratis as I and anyone can download it for free, but not libre as I cannot use it for all lawful purposes due to non-commercial clauses. ... Not only do they forbid bulk download of the vast majority of the content.
  18. Elsevier's new API approach to Content Mining should be avoided…

    https://blogs.ch.cam.ac.uk/pmr/2014/06/10/6054/
    17 Jan 2022: APIs or other download mechanisms when the website in question holds a lot of content. ... We also know, for example, [that researchers would like to mine third-party images and graphics that they cannot currently download automatically via our API].
  19. APE2008 more thoughts | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/01/30/ape2008-more-thoughts/
    17 Jan 2022: 1 million authors, over 1 billion article downloads. The primary motive of authors is to disseminate their ideas (it’s reassuring to know that as we can plan new ways of
  20. https://blogs.ch.cam.ac.uk/pmr/tag/fortran/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/tag/fortran/feed/index.xml
    17 Jan 2022: of version 3.1br / This is to announce the release of version 3.1 of the FoX library.br / (download from <a
  21. Open APIs: fundamentals and the cases of KEGG and Wikipedia |…

    https://blogs.ch.cam.ac.uk/pmr/2011/09/16/open-apis-fundamentals-and-the-cases-of-kegg-and-wikipedia/
    17 Jan 2022: through a standardized open API or via download from a standard specified location). ... The only change will be to FTP access. We have already introduced a “Download KGML” link for the KGML files that used to be available only by FTP, and will
  22. Dissemination of CrystalEye | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/31/dissemination-of-crystaleye/
    17 Jan 2022: I think this is true of Pubchem – anyone can download individual entries and re-use but it is required (and common courtesy) to ask before downloading the whole lot. ... I think this is true of Pubchem – anyone can download individual entries and
  23. OREChem | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/03/27/orechem/
    17 Jan 2022: For example if you go to this blog address and download it, what do you get.
  24. Bioclipse – Rich Client | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/05/25/bioclipse-rich-client/
    17 Jan 2022: So NASA wrote their own and you can download it and run it locally.
  25. 5 Years of Open Babel | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2006/11/26/5-years-of-open-babel/
    17 Jan 2022: Should downloads count as citations?). Actually I’m not sure that helping open source software is that highly regarded in academia either, is there a perception Open source=Free= Of little ... Should downloads count as citations? They don’t for
  26. "should theses be Open?" | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/03/29/should-theses-be-open/
    17 Jan 2022: microfilm’ system – and the downloads of digitised theses far outstrip the previous supply figures.
  27. https://blogs.ch.cam.ac.uk/pmr/tag/blog/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/tag/blog/feed/index.xml
    17 Jan 2022: I hope that the blog will be a better format for general discussion.br / The SVN repository is the primary resource besides the downloads.
  28. FORCE2015 Workshop: How ContentMine works for you and what you can…

    https://blogs.ch.cam.ac.uk/pmr/2015/01/08/force2015-workshop-how-contentmine-works-for-you-and-what-you-can-bring/
    17 Jan 2022: No programming experience required but bring a lively mind. It will help if we know how many are coming and if you download the virtual machine beforehand, jsut to check it ... works. easy, but takes a bit of time to download 1,8 GB.
  29. Comments from chemspider | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/04/24/comments-from-chemspider/
    17 Jan 2022: A Scientist and the Web. Comments from chemspider. Posted on April 24, 2007 by pm286. Chemspider writes: –. Name: Monkey at Development | E-mail: valt@chemspider.com | URI: | IP: 68.33.203.5 | Date: April 24, 2007. Peter, good catch – thanks for
  30. Leo Waaijers: DARE to Inspire | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/03/14/leo-waaijers-dare-to-inspire/
    17 Jan 2022: I could download one and within a minute[] OSCAR had read much of the chemical data from it.
  31. Chemspider and Pubchem – open data | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/11/30/chemspider-and-pubchem-open-data/
    17 Jan 2022: If Chemspider allows the direct download and re-use of their data from their site then I also congratulate them. ... Not sure, but the FTP download does not contain links to other databases though.
  32. Comments on the NIH policy | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/05/30/comments-on-the-nih-policy/
    17 Jan 2022: A public satement of this would be very valuable. Secondly that it will not impose server-side limitations of robotic downloads.
  33. Repositories or Lists of Open Molecules | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/04/29/repositories-or-lists-of-open-molecules/
    17 Jan 2022: By Open I mean that anyone can, in principle download, copy or clone part or all of the site, re-use the information and redistribute without reference to the original site. ... We ask that users who download significant portions of the database cite the
  34. https://blogs.ch.cam.ac.uk/pmr/tag/html/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/tag/html/feed/index.xml
    17 Jan 2022: and want to read the file, download the zip file, unzip it, point your browser at it, swear at me when the browser breaks.br / [UPDATE: Bill says is breaks.
  35. Towards a manifesto on Open Mining of scholarship | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2012/05/01/towards-a-manifesto-on-open-mining-of-scholarship/
    17 Jan 2022: Universities create caches to avoid repeated downloads but publisher want the downloads so they can count-the-clicks.
  36. Does “Open API” mean anything? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2010/08/29/does-open-api-mean-anything/
    17 Jan 2022: Unless you are SureChem Pro or PDF subscriber, you may not download, store (in any medium) or transmit the material contained on this Web Site. ... There is no algorithm to expose the whole data. By contrast you can, in principle, download the whole of
  37. Open Data: help from Microsoft | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2006/12/12/open-data-help-from-microsoft/
    17 Jan 2022: The add-in downloads the Creative Commons license you designate from the Creative Commons Web site and inserts it directly into your creative work. ... You cannot patent data. So let’s encourage everyone to download this plugin.
  38. Enjoyable version control with the Tortoise | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2006/10/30/enjoyable-version-control-with-the-tortoise/
    17 Jan 2022: It tells you when they are out of synce and whether you need to upload a file TO the server or download someone else’s update FROM the server. ... If so it will download them to my directory and merge them.
  39. Content-mining: #animalgarden write a crawler | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2013/12/14/content-mining-animalgarden-write-a-crawler/
    17 Jan 2022: C: But #ami2’s very fast. She doesn’t need to wait. G: If she tries to download papers too quickly – like 1000 per second –it might confuse our servers. ... It only downloads things. G: So will it download my articles?
  40. Kitware: Liberation Software | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2013/02/26/rds2013-managing-research-data/
    17 Jan 2022: Happy ending? Who knows. A garden is walled if you cannot fork, or download the whole contents.
  41. https://blogs.ch.cam.ac.uk/cosblog/feed/index.xml

    https://blogs.ch.cam.ac.uk/cosblog/feed/index.xml
    17 Jan 2022: download and use, so no one will need to pay for annual renewals to get access to new releases any more.
  42. I ask Elsevier for their list of articles published as “hybrid Open…

    https://blogs.ch.cam.ac.uk/pmr/2012/07/27/i-ask-elsevier-for-their-list-of-articles-published-as-hybrid-open-access/
    17 Jan 2022: I wish to download and analyze all of them. Thanks in advance for your answers. ... If you would like to conclude our earlier discussion about a bulk data download to facilitate your text mining, please do let me know.
  43. ePUB is a revolution in scholarly publishing. We explore…

    https://blogs.ch.cam.ac.uk/pmr/2014/01/04/epub-is-a-revolution-is-scholarly-publishing-we-explore-biomedcentrals-offering/
    17 Jan 2022: see and chrome://epubreader/locale/welcome.html ). Go to the webpage where you want to download the ePub file and click on the download link. ... Now EPUBReader starts working: it downloads/opens the ePub file, uncompresses it and does some other
  44. ACS Open Choice allows full re-use | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/03/25/acs-open-choice-allows-full-re-use/
    17 Jan 2022: ACS Open Choice articles are fully open access in the sense that the licence [PDF link] allows users – for non-commercial research and education purposes – to “access, download, copy, display and
  45. How to share data and how not to | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/07/16/how-to-share-data-and-how-not-to/
    17 Jan 2022: Perhaps also there could be a download package for all this as zip, tar.gz etc…. ... However, there is no Download as XML for the table, like there is not at the other link.
  46. #IUCR2011: Open Crystallography | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/08/28/iucr2011-open-crystallography/
    17 Jan 2022: By open data in crystallography we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to software or use
  47. #solo10: GreenChainReaction – volunteers start to process patents |…

    https://blogs.ch.cam.ac.uk/pmr/2010/08/31/solo10-greenchainreaction-volunteers-start-to-process-patents/
    17 Jan 2022: The steps are simple:. Download the software and ancillary files. Download some patent indexes. ... Can you post links for the relevant steps you outline? For example, where do I download the software and ancillary files?
  48. https://blogs.ch.cam.ac.uk/pmr/tag/ore/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/tag/ore/feed/index.xml
    17 Jan 2022: For example if you go to this blog address and download it, what do you get.
  49. What is civil disobedience? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/07/27/what-is-civil-disobedience/
    17 Jan 2022: A Scientist and the Web. What is civil disobedience? Posted on July 27, 2011 by pm286. I have already blogged about the Aaron Swartz case and civil disobedience
  50. The high cost of the lack of open data | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/03/26/the-high-cost-of-the-lack-of-open-data/
    17 Jan 2022: You can download the full study from the Department for Business, Employment and Regulatory Reform’s website here.
  51. #vivo12 What I might be going to say | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2012/08/23/vivo12-what-i-might-be-going-to-say/
    17 Jan 2022: Please try not to download movies during my presentation. More later I hope.

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