Sunday, January 13, 2013

Ten simple ways to share PDFs of your papers #PDFtribute

There is a spreading surge of PDF sharing going on in relation to a tribute to Aaron Swartz who died a few days ago.  For more on Aaron and tributes to him see the collection I am making here: The Tree of Life: RIP: Aaron Swartz.  For more on the PDF sharing see this CNET story for example: Researchers honor Swartz's memory with PDF protest and

I should say, sharing your PDFs is not necessarily clearly not enough (the license on the PDF may affect what people can do with them if they feel constrained to follow the law).  It is also critical to think about the level of openness of a paper, but I will save most of the comments on that for another time. What I wanted to do here is point out various ways to share PDFs for people who don't know how ...

UPDATE 1/14: See follow up post 10 things you can do to REALLY support #OpenAccess #PDFTribute

Ten simple ways to share PDFs of your papers.

1. Publish your paper in a fully #openaccess journal (so called GOLD OpenAccess).

Such journals immediately post your paper online for all to see and frequently also post your paper in various formats to repositories like Pubmed Central.  For a list of such journals see the "Directory of Open Access Journals".  In my opinion, this is the best, and, well, really only viable long term option.  This is what I do for papers from my lab.
2. Publish your paper in a non #openaccess journal that has the option of selecting / paying for #openaccess on a case by case basis. 

Many journals that are not fully #openaccess have the option of paying extra to have your paper be published in an #openaccess manner and then the journal handles not only posting the paper on their site but also frequently depositing in a repository of their or your choosing.  UPDATE: Note - in many cases the licenses used by journals for such one-off "open" publishing are not fully open, despite what some of the journals claim so proceed with caution (see PLOS Biology: Why Full Open Access Matters for example).

3. Publish in a non #openaccess journal that releases papers to a repository after a delay.

Many journals put papers behind a paywall initially but then "free"them up in some way after a set period of delay.  For example a large number in biomedicine will deposit papers to Pubmed Central and also make them freely available on their website after 6 months.  Frequently as with #2 above, the licenses associated with such release of papers are not fully open, but this is a way to have your papers be at least accessible to others after a period of time.

4. Deposit your paper in a preprint server before you submit it for publication.  

For more on preprint servers see
Examples of commonly used preprint servers include
5. Self-archive your PDF in a repository (so called GREEEN OpenAccess).

Various repositories out there exist for posting ones papers.  They work in essence like a preprint server though some people use them more for posting papers after they have been published so I am listing them separately here.  More detail on self-archiving can be found here.  A good source of information about repositories is the Registry of Open Access repositories.  Also the Directory of Open Access repositories.  Another good source is SPARC. Also see here.

One repository commonly used in biomedicine in Pubmed Central.  Alas one is only allowed to post papers there by oneself if the work in the paper was funded by an NIH grant.

Another approach is to use arXiv as a repository where you can post things even after they are published.

Another growing venue for self-archiving is an institutional repository.  As many universities expand their commitment to open access or access university repositories are becoming a source of more and more publications.  Check to see if your institution has a repository and use it.

UPDATE: Note, just depositing your paper in a repository or preprint server does not necessarily mean your paper is open access.  Look in detail at the license and copyright policies of the archives you are considering before using them.

6. Self post your PDFs to a website you control.

If you do not have a personal website and/or do not know how to post a paper to your website, well, you should learn more about this.  A few simple ways to quickly post a PDF for others to get access to include

Create a new blog / website with a system that allows posting PDFs.  There are many many options for this.  One is Posterous.  Another is Wordpress.Com.  There are certainly a million other ways.  Upload a PDF to Google Docs and then share the Google Doc link.  Post to Dropbox and share the link there.  Etc. etc. etc.  I ended up using Wordpress.Com to create my lab page and to post all my PDFs.

7. Post your PDFs to an online reference collection.

Many systems now exist for collecting and collating and sharing reference collections online.  They include CiteULike, Zotero, and Mendeley.  I particularly like Mendeley right now in part because it makes it very easy to share PDFs privately or publicly.  I for example have posted all my own papers on Mendeley as well as papers of my father's (for more on this see The Tree of Life: Freeing My Father's Publications and Free Science, One Paper at a Time | Wired Science |

8. Create an academic profile page and post PDFs there.

Many systems now exist for creating a personal Academic profile of sorts.  One example is Academia.Edu. I have created a page here  Jonathan Eisen | University of California, Davis - although I confess I have not been updating it much.

9. Post to Slideshare.

Though many people end up only posting slideshows to Slideshare, and I use it for that purpose, I have posted many of my papers there as well. See for example:


10. Post to "Data" archives.

There is a large growing collection of places to post "Data" to share it with others.  Some of these sites also allow posting of papers.  For example, I have posted multiple papers to Figshare, a great data sharing site that can be used to post and share just about anything. I have also used Figshare for this (for example - here is my PhD thesis there).

11. Ask a Librarian. (Yes it goes to 11)

Probably the best way to figure out how to better share your PDFs if the options above don't work for you (or even if they do) is to talk to a librarian.  They are the most knowledgable people in regard to methods and systems and other issues for sharing academic work.

Some related posts from The Tree of Life

Other ideas? Please post in comments ...


  1. A great share. Thanks.

    Aaron H. Swartz

    (November 8, 1986 – January 11, 2013)

    The news about his death are really sad.


    We need to stop to hunt people, who are trying to help to move into the digital age.

    "At the time of his death, Swartz, if convicted, faced a maximum of $1 million[42] in fines and more than 35 years[42] in prison after the government increased the number of felony counts against him from 4 to 13.[43]...."

    On July 19, 2011, Swartz was charged by U.S. Attorney for Massachusetts with wire fraud, computer fraud, unlawfully obtaining information from a protected computer, and recklessly damaging a protected computer, in relation to downloading roughly 4 million academic journal articles from JSTOR.[26] According to the indictment against him, Swartz surreptitiously attached a laptop to MIT's computer network, which allowed him to "rapidly download an extraordinary volume of articles from JSTOR."[27] Prosecutors in the case claim Swartz acted with the intention of making the papers available on P2P file-sharing sites.[28]
    Swartz surrendered to authorities, pleading not guilty on all accounts, and was released on US$100,000 unsecured bail.[29][30] Prosecution of the case continued, with charges of wire fraud and computer fraud, carrying a potential prison term of up to 35 years and a fine of up to $1 million.[31][32] After Swartz's arrest, JSTOR put out a statement saying it would not pursue civil litigation against him.[29][33]
    Despite JSTOR having dropped all civil charges, Assistant U.S. Attorneys Stephen P. Heymann and Scott L. Garland[34][35][36] pursued the criminal case against Swartz under U.S. attorney Carmen M. Ortiz, who justified the charges by stating "stealing is stealing, whether you use a computer command or a crowbar, and whether you take documents, data or dollars."[29] The case tested the reach of the Computer Fraud and Abuse Act, which was passed in 1984 to enhance the government’s ability to prosecute hackers who accessed computers to steal information or to disrupt or destroy computer functionality.
    The government, however, has interpreted the anti-hacking provisions to include activities such as violating a Web site's terms of service or a company's computer usage policy, a position a federal appeals court in April said means "millions of unsuspecting individuals would find that they are engaging in criminal conduct." The 9th US Circuit Court of Appeals, in limiting reach of the CFAA, said that violations of employee contract agreements and Web sites' terms of service were better left to civil lawsuits.
    The rulings by the 9th Circuit cover the West, and not Massachusetts, meaning they are not binding in Swartz's prosecution. The Obama administration declined to appeal the ruling to the Supreme Court.[37][38]"
    I am starting to think, that Aaron might not got the public support he had needed after he came in big trouble. We might need more solidarity in social networks.

  2. any advice for young scientists (people who don't have their own labs yet, but hope to)?

    It's pretty tough out there and the necessity of Nature-Science-Cell is drilled into our heads early. The general advice I receive is to publish well and early, start a lab, then join the open-access fight.

    Are there alternatives that you'd suggest? or articles on this that I may have missed?

    1. The Nature-Science-Cell thing is a pile of bull shit. What is the evidence that this is the route to a job, grants, fame etc? The route is to do good work, to publish it, and to present it and get people to read it and/or hear it. Sure, if you publish a few papers in one of the vanity journals it can make it easier for you to get looked at, but if you do lame work you usually still won't get a job or tenure.

    2. One very interesting alternative is to publish in you pay a $100 fee an can publish 1 open access article/year for life

    3. One very interesting alternative is to publish in you pay a $100 fee an can publish 1 open access article/year for life

    4. Maybe we should give Aaron a bronze statue like Joe Paterno.

      After all, a crime is a crime...

  3. I'm not a scientist (I'm a writing teacher), but I saw your blog post when someone shared it at Google+ and it inspired me to put the download links for my various book PDFs all together in one place. I linked to your post and included your nice graphic; I hope you don't mind my reuse of the graphic - "tree of life" seems a very appropriate metaphor at this moment. Here is my post, and I will go share your post over at my university's Chatter to spread the word. Thank you for this.

  4. In so far as "the necessity of Nature-Science-Cell" is a real thing at all, it's only a thing because we researchers reinforce it. We need to just grow up and stop participating in the hallucination that quality of research is determined by, or even correlated with, the journal it appears in -- especially when that journal requires the research to be sliced, diced and pureed to fit within ludicrously small pagecounts.

    Nature, Science and Cell are poison. Stop drinking it, and stop encouraging other people to.

  5. Interesting about number 11. I'd like librarians to take an active interest in archiving my work, including my lab notebook (which is openly published, as I go) and my work published old style. But they seem to offer no services for this.

    Who do you have archiving and preserving this blog?

    1. hah - well - it was a bit of wishful thinking --- maybe I should have said "In an ideal world, librarians should be able to help ... but it depends on which ones you interact with ..."

    2. Librarians are usually more than happy to help the users with their various requests. They are (or at least should be) involved in the promotion of open access, creative commons, etc. Maybe for now it especially come from younger librarians (and academic-related fields I would say). Many questions remain unanswered too about archiving and personal digital material. Still, you should try to ask to your librarian (or others) even if those services are not promoted. If it is not offered, we usually DO like to search to please users and improve ourselves!

      -Jacynthe, medical librarian

    3. I'd like to second Jacynthe in saying that many librarians have the expertise and willingness to help researchers at every step of the research process, including archiving and preservation. Here at the UCs, the library also supports a number of services to help researchers preserve and share their work, like eScholarship (an open access publishing platform) and Merritt (repository for digital content, including data sets or lab notebooks).
      - Lisa, UCLA Biomedical Library

  6. Related to lab notebooks, an interesting project from UC Berkeley that their library is a part of is their Research Hub . It is a shared *temporary* workspace that is part file management, part project collaboration, part dept resource tool, part research data management. When the project is concluded the data and components you want to preserve for the long term can be uploaded with the click of a button to Merritt for long term preservation and access. - Tony Aponte, UCLA Science and Engineering Librarian

  7. Seconding what my colleagues above said that if you are in the UC system, you can also post your papers for free to eScholarship:

    Also, I am a UCD librarian, and I am more than happy to try and help anyone here who wants to explore these issues and publish their work openly :) It is true that we are just starting to offer services, but we do want to help! (contact me at

    I also knew Aaronsw slightly, and he was spectacular. He will be missed.

    1. Phoebe --- most of the people who read this are not from UCD so you may be inviting all sorts of "outsiders" (not that there is anything wrong with that ...)

  8. Great Blogpost. I've strated sharing my Documents on, in order to have more of a magazine look and feel. The HTML5 Player is great: You don't need the Flash Plugin to look at a document

  9. Use this hashtag #sharecredentials to share your credentials for limited-access database


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