The Self-Journals of Science

      An open curation platform with repository and peer-review services

Uploading an article

Only registered members can upload an article. When you are logged in, a button "Upload an article" button becomes available in the top bar. Articles are uploaded by one member on behalf of his/her coauthors. The goal of the process is to create a PDF and interactive HTML version that are accurately classified in SJS.

There are 5 steps for uploading an article:
The author responsible for the upload will can then revise the article.

1. Enter metadata and upload source files

The metadata are as follows:
  • Article type (e.g. research article, review article...)
  • Title
  • Abstract
  • Authors and their affiliation(s). You can add coauthors who are not members of SJS. However, as SJS cannot certify their agreement (or even their existence), they will be tagged with "Unregistered and unverified coauthor" in the final header of the article. The affiliation(s) of a registered coauthor can easily be selected from affiliations declared in his/her account. The affiliation(s) of an unregistered coauthor must be individually entered (with the help of the word completion).
  • Keywords from the Tree of Knowledge

Keywords are an important way to sort and extract data on SJS. The article must be accurately tagged with all relevant keywords to help readers find it easily. You are advised to tag articles with i) the scientific field(s) of the article and ii) the specific topics covered in the article. Authors should explore the Tree of Knowledge before uploading to check for the keywords they need. If important and necessary keywords are missing, authors should add them into the relevant part of the Tree.

The source files should be:
  • A single .tex file containing the main text of the article, written in LaTeX format. This file should not include the metadata of the article as this data is handled separately. The syntax of the .tex file is not entirely free and must comply with certain constraintsthat are listed in this manual.
  • any figures in the article must be in .eps, .pdf, .jpg, .png or .gif format
  • any external bibliography of the articles must be a .bib file. It is also possible to upload a custom .bst file.
  • all supplemental files, in any format
  • an abstract graphics which must be in .jpg, .png or .gif format. You are strongly advised to provide an abstract graphics since this will make the article more appealing.

For non-LaTeX users

If you are not a LaTeX user, don't despair! There are at least two ways to get your article into the requested .tex format farily quickly and without too much difficulty.
1. The easiest is to request our help. Contact us at michael@sjscience.org with object "Help with Latex".
2. The other way is to follow the easy-to-use tutorial we have designed. Most people should be able to format their article in 2-3 hours and learn LaTeX in the process. It has been successfully tested by other non-LaTeX users. After 20 minutes of inevitable confusion, you will soon get it and will be copy-pasting your text article into the correct LaTeX building blocks. You may well ending up preferring LaTeX rendering over your current format! Simply follow these steps:
  • Download and unzip these tutorial files. Open SJS-Latex-Tutorial.tex with any text editor and do not be afraid!
  • Create a free account at ShareLatex (www.sharelatex.com) and start a New Project (choose "Blank project").
  • ShareLatex creates a default file "main.tex". Copy and paste the content of SJS-Latex-Tutorial.tex into this main.tex file(overwriting its current content). Upload all 3 .jpg and the .bib files by clicking in the top left-hand corner).
  • Click "Recompile" (top right-hand corner).
  • Have a look at the preview and download the .pdf file generated by clicking in the top right-hand corner). The preview is not perfect (e.g. you cannot see italics, mathematical notation is flawed) but it is very convenient: you can double-click anywhere to bring up the associated part of the .tex file.
  • Now you can start adapting your article. Read the helpful comments that start with the % symbol in the main.tex file (they should appear in green). Upload your own image files and bibliography (in .bib format). Gradually insert your own text at line 62 and copy &#amp; paste all the features you need from the rest of the tutorial file. Recompile often to check that LaTeX understands what you are doing. If not, a red sign will appear at the top of the preview and you will get a comprehensive bug report. To successfully upload your article to SJS, there must be no red sign. Orange signs are warnings that generally can be ignored. The other thing is to regularly download and check the .pdf version of your article.

2. Confirm article header and preview

The article header and preview are generated from the metadata and abstract graphics. If anything is wrong, you can go back to the previous step to make necessary changes.

3. Validate the PDF and HTML output

In this third step, the PDF and the HTML versions of the article can be previewed. An interface is available to edit the source .tex file online, if necessary.
If PDF generation failed, the compilation log will be made available and the HTML will not be generated. If you are stuck at this stage and cannot fond the problem yourself, contact michael@sjscience.org
If PDF generation succeeds, the HTML version is generated. You can check it and edit the source code if needed. SJS gives you as much assistance as it can in this process by pointing out any "risky" syntax we can detect. Note that there may be more problems than the ones SJS reports, so you should definitely check the whole HTML output.

4. Get all coauthors to validate the article

This step gives you a preview of the webpage that will be created to host your article. All your coauthors must validate this preview before the final step. When the process reaches this step, the article will be available as an unpublished item in the "Articles" section of your personal account and each coauthor's account. This gives your coauthors access to the preview so they can validate it personally. When all coauthors have done this, you can move on to the final step.

5. Invite readers

In this final step, you invite peers to read your article. The point is that they may become reviewers, which will bring life to your article and give it more visibility. You can invite other members of SJS by selecting their name. You can also invite non-members by entering their e-mail address. You should think carefully about who you want to invite before this final step. It is important not to invite only the few leading specialists of your field: in SJS, articles are not seen as valid because two individuals have decided it is valid, but because there is an observable community-wide consensus around it.

After final validation, the current date will become the publication date of your article on SJS. Later, you can still invite more readers later on and promote your article as you think fit.

6. Revise article

The revision process is not yet fully automated. For now, it is only possible with our help. Contact us at michael@sjscience.org, putting “Revision” in the subject line.

Personal account

Your personal account has a public and a private view. The public view displays your profile and your scientific activity in its three dimensions through four tabs, whose titles are self-explanatory : Profile, Articles, Reviews/Discussions/Prioritizations and Self-Journal. The private view of your account can only be accessed when you sign in and click "My account" on the top bar. The "Self-Journal" tab then allows you to build your own self-journal. You can also access to one more tab called "Settings & Following options". This tutorial gives further details on these two tabs below.

Self-Journal

In public view, this tab can be used to browse issues of the the account owne's self-journal that have already been published. In private view, this tab is used to privately build the current issue of your self-journal. You can publish it by clicking on “Preview this issue” then “Release this issue”. The first button becomes is enbaled when your current issue has a title, an editorial, at least one keyword and at least 4 articles. In the current stage of development of SJS, you cannot edit an issue after you have published it. Besides the selection of articles you present, the scientific value of your self-journal also lies in the comments you include, so it is in your best interest to provide some!

There are two ways to add an article to the current issue :
  • If the article is available on SJS, just import it by clicking “Add to my journal” in the left sidebar on the article page.
  • Otherwise, click the “Add external article” button and provide the metadata of the article : title, URL or DOI, at least the first author (it could be “first-author et al.” if you do not want to copy all of them) and publication date. There are two other optional fields: the abstract and abstract graphics (.jpg or .png) to improve the layout of your self-journal. Authors must be entered as follows :
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The following item will be created so that you can order and comment on your selection of articles.

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a) Drag and drop the arrow symbol to change the order of articles. After publication, the layout of your issue will especially highlight the first article.
b) Remove the article from the current issue
c) Comment on the article.

Settings and following options

This important tab gives you a powerful tool to automatically monitor scientific activity on SJS in a highly customized way.
You can follow i) the activity of other members, ii) activity around given articles, iii) the release of new journal issues and iv) automatically run topical queries. You can decide how frequently SJS should send you activity reports. Importantly, the SJS policy is not to spam users. We are very aware that a scientist's mailbox tends to be overloaded with irrelevant information, so we want to ensure that any e-mail from SJS is worth reading. In particular, when no recent activity matches your queries, SJS does not spam you with an empty report. You can therefore use this powerful tool with confidence since you will get nothing other than what you have explicitely asked for.
  • You can set the frequency at which most recent query results are aggregated and reported to you.
  • To follow an article, you click "Follow this article" on its page. This will create an item in the section "Followed articles". You can then select which events are reported to you about that article : revisions, new reviews, new discussions.
  • To follow members or subscribe to their self-journals, you must click on the relevant buttons in their account (to the right of their picture). This will create an item in the "Followed articles" or "Subscribed journals" section. Again, you can select which type of member-related activity is reported to you: new articles, prioritizations, reviews, discussions.
  • You can ask SJS to automatically run queries and report new results. You need to complete a query in the "Search" engine of SJS and click "Save this query". After naming the query, it will appear as an item in the "Saved search queries" section. From there, you can i) manually run this query by clicking the corresponding item or ii) have SJS run it automatically by checking the box "Report new results".

The Tree of Knowledge (ToK)

The Tree of Knowledge is a consensual structured vocabulary that is used to map all scientific activity on SJS (and later, on all the Web). When properly tagged with keywords from the ToK, data can be extracted from SJS easily, exhaustively and unambiguously without artificial intelligence algorithms. There are two types of links between keywords in the ToK: a "Narrower concepts" link (which can be thought as a “parent-child” link) and a "Related concepts" link which connects keywords from distant parts of the ToK (and which can be thought as a "cousin" link). These links can be used to browse scientific knowledge in a logical and intuitive way. The Tree of Knowledge is self-managed by SJS users, who add new keywords and new links between keywords.
Note: there are known conflicts between the ToK and some combinations of browsers and antivirus software. If the ToK does not display correctly on your computer, please consider using an other browser. We are working on solving all these conflicts in the long term.

Main ToK interface

The main interface is accessed by clicking "Tree of Knowledge" in the top bar. This interface can be used to manage keywords and browse of the ToK

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1) Current keyword
2) Narrower concepts of the current keyword. Click on any of them to go deeper into the ToK.
3) Related concepts of the current keyword. Although related to the current keyword, these keywords belong to another branch of the ToK.
4) Parents of the current keyword. Click on any of them to go higher in the ToK.
5) List of synonyms of the current keyword
6) Number of articles, members, journals, tagged with the current keyword. Clicking on any of these items launches the associated query in the search engine
7) After signing in, you can suggest a new narrower concept for the current keyword by clicking this button. This new keyword will be open to voting (see 9)
8) After signing in, you can suggest a connection between the current keyword and another one which already exists elsewhere in the ToK. Start writing the target keyword and select it in the autocomplete menu, then click “Create link”. This new connection will be open to voting.
9) Newly proposed keyword. After signing in, you can vote it up or down.
10) Keywords quicksearch

Pop-up version of the ToK

The ToK also has a pop-up version that is openeed by the "Pick keywords" button, which is available in various contexts on the website (such as the search engine). This interface can be used to select keywords by clicking on the + symbol in front of them (1). The list of currently selected keywords is displayed at the bottom of the window (2).

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Article Page

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The article page displays the article's content and metrics (1) and can be used for peer review (2). The left sidebar (3) provides a number of additional features.

Peer review and discussion interface

A + button is attached to each paragraph and figure. This will open the following interface :

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This interface contains two forums "Critiques" and "Comments" (1), specifically dedicated to the paragraph or figure. Only signed-in members can write in these forums. Each forum can contain many threads. A new thread can be created by clicking "New thread" (2). Each thread may contain multiple replies (3); these can be expanded by clicking "See all replies". You can use mathematical notation by including LaTeX code between two $ signs(4). Every post in these forums is signed, dated, recorded in its author's account (5) and can be evaluated through a +/- vote (6). Every user can click these buttons once only. The purpose of these buttons is to highlight the most relevant reviews (i.e. most relecant to the article's authors and to other readers) and to dissuade and filter out irrelevant ones. These votes must be used in connection with the sort options: posts can be sorted by date, by vote + and by vote - (7).

General critiques or comments of the article should be posted in the forums attached to its abstract.

Article metrics

There are three important metrics on SJS: validity, importance and priority.

Validity is determined by a community-wide choice between two possibilities displayed at the top of the article: "The article has reached scientific standards" and "This article still needs revision". When signed in, you can click on one of these buttons. The counters will be incremented and your name will be added to the public list of voters. Importantly, you can later change your mind: you can still click on the other button and your new vote will replace the previous one. SJS should not and does not provide any definition of "scientific standards". Rather, scientific standards are dynamically self-defined by the community, by stating which articles have acheived them and which ones have not.

The importance of the article is reflected by the number of curators. This metric is displayed in the left sidebar. It counts the number of SJS members that have curated the article in at least one of their self-journal issues.

Priority is a measure of the short-term appeal of the article. Priorizing an article simply sends the signal to the rest of the community that, for some reasons (be it positive or negative), this article requires attention. Clicking "Prioritize" increments the counter and add your name to the public list of members who did the same. Following the article or exporting it to your self-journal automatically prioritizes the article.

Left sidebar

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    Add to my self-journal: when signed in, this feature creates an item in the Self-Journal tab of your account.
   Also prioritizes the article (unless you have already done so).

   Follow this article: when signed in, this feature creates an item in the Settings & Following Options tab of your account.
  Also prioritizes the article (unless you have already done so).

  Critiques X+Y: X is the total number of threads opened in the “Critiques” forum and Y is the number of replies.

  Comments X+Y: X is the total number of threads opened in the “Comments” forum and Y is the number of replies.

  Supplemental files: the source files of the article and any supplemental file uploaded by the authors.

  All Critiques and comments: displays all critiques and comments posted for this article.
  The main purpose of this feature is to give a quick overview of the “hot spots” in the article, as well as filtering options .

  Article outline: lets you browse quickly through the different sections of the article

FAQ

1) How to follow science on SJS?

This question spans two aspects:
i) Staying informed of the latest articles that are relevant to you.
ii) Understanding the different focuses and trends in your field.

SJS provides easy and highly automatized ways to follow science comprehensively and with minimal noise. The following points help you get the most out of SJS:
  • Follow the scientific activity of your peers:
  • i) Articles they upload to SJS
    ii) Their reviews and discussions
    iii) Articles they prioritize
    Just click "Follow XX" on the personal page of a peer and select which aspects of his/her activity you want to follow in your "Settings and following options".
  • Follow the activity around an article:
  • i) reviews
    ii) discussions it has generated.
    iii) revisions
    Click "Follow this article" and fine tune your "Settings and following options".
  • Keep up to date with topics using the SJS Tree of Knowledge feature:
  • i) Get direct access to associated articles and scientists
    ii) Set up a keyword alert the SJS search engine with the "Save query" feature.
    You should check the Tree of Knowledge regularly to see whether new keywords have been added to your field of interest.
  • Subscribe to your peers' self-journals and publish your own self-journal to spread your vision within your community.
In short :
1) Use the automated systems offered by SJS to keep up to date with the activity of peers, articles, topics and journals.
2) Periodically check the Tree of Knowledge for new keywords associated with your field(s) of interest.

2) Is the content of SJS secure? Will it survive a thermonuclear war?

For now, we can just give you the same answer as every other host, i.e. "We do the right things, just trust us". However, in line with our goal to make Science the responsibility of all scientists, and as SJS grows, we will implement a shared storage solution where every user can dedicate a small part (e.g. 100Mb) of their own hard-disk space to store a part of SJS content. Hence, it will be copied hundreds of times all around the world and we will be able to prove that it is indeed secure. Again, if we as scientists take responsibility, we will come up with something better and cheaper than any other solution.

There is a free software initiative being developed to prepare for this move: http://ceph.com . If you have some relevant skills, please go and help them! The solution currently works but it is not yet user-friendly enough to install and configure.

3) How should I cite an article from SJS?

Authors, title, date, version number, URL.

You will need to mention which version you had access to since authors may still modify their article after you have cited it.
If an equivalenttt version of the article has been published in an academic journal, please cite this primarily as the authors should not be deprived of their traditional indexation in the current publish-or-perish system. Ideally, cite both. Citing an article from SJS is genuine. On SJS, the value of an article is determined in other, novel ways.