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 logged in, a button "Publish an article" becomes available in the top bar. This process is conducted by one member on behalf of his/her coauthors. The goal of the process is to create a PDF and HTML version accurately classified in SJS.

The uploading of an article takes place in 5 steps :
The author responsible for the upload will then have the possibility to revise the article.

1. Metadata entry and source files upload

The metadata are:
  • The article type (e.g. Research article, review article...)
  • The title
  • The abstract
  • The 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 be simply selected among the ones 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

These keywords are an important way to sort and extract data on SJS. The article must be accurately tagged with all relevant keywords so that its audience easily finds it. It is recommended to tag articles with i) scientific field(s) involved in the article and ii) accurate topics covered in the article. Authors are expected to explore the Tree of Knowledge before the upload process 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 are:
  • A single .tex file containing the main text of the article, written in the LaTeX format. This file needs not and should not include the metadata of the article as they are processed separately. The syntax of the .tex file is not entirely free and must obey some constraints listed in this manual.
  • if any, all the figures of the article in a .eps, .pdf, .jpg, .png or .gif format
  • if any, the external bibliography of the article as a .bib file
  • if any, all supplemental files
  • an abstract graphics in .jpg, .png or .gif format. It is strongly recommended to provide an abstract graphics since it will make the article more appealing.

For non-LaTeX users

Non-LaTeX user, do not give up! You have at least tow ways to get your article in the requested .tex format within the next hours without suffering.
1. The easiest is to request our help. Contact us at support@sjscience.org with object "Help with Latex".
2. The other way is to go through the efficient tutorial we have designed. We expect most people to be able to format their article in 2-3 hours with it and learn a bit of LaTeX in the process. It has been successfully tested by other non-LaTeX users. After 20 minutes of inevitable confusion, you will get it and will be quickly copy-pasting your text article in the correct LaTeX building blocks. In the end, it is even possible that you prefer LaTeX rendering over your current one! 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-paste the content of SJS-Latex-Tutorial.tex into this main.tex (i.e. by replacing its current content). Upload all 3 .jpg and the .bib files by clicking (at top left).
  • Click on "Recompile" (top right).
  • Have a look at the preview and download the generated .pdf by clicking (at top right). The preview is not perfect (e.g. you cannot see italics, mathematical notation is flawed) but very convenient: double-clicking somewhere on it brings you to 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 (they should appear in green). Upload you own image files and bibliography (in .bib format). Insert gradually your own text at line 62 while copy-pasting all the features you need from the rest of the tutorial file. Often click on "Recompile" to check if LaTeX understands what you are doing. If not, a red sign will appear at the top of the preview and you will have a comprehensive bug report. To successfully upload your article on SJS, there must be no red sign. Orange signs are warnings that can be generally ignored. Also regularly download and check the .pdf of your article.

2. Validation of the header and the "teaser" of the article

The header and teaser of the article are generated from the metadata and the abstract graphics. A preview is displayed. If something is wrong, you can go back to the previous step to perform the relevant modifications.

3. Validation of the PDF and HTML output

In this third step, the PDF and the HTML versions of the article can be previewed. An interface allowing for the online editing of the source .tex file is available.
If the PDF generation failed, the compilation log will be available and the HTML will not be generated.
If the PDF generation succeeded, the HTML is generated. You can check it and modify the source code if needed. We will give you as much assistance as we can in this process by pointing all the inappropriate syntax we can detect. Note that there may be more problems than the ones we report, so you should definitely check the whole HTML output.

4. Validation by all coauthors

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" of your personal account and of each coauthor's. This is the way your coauthors have access to the preview and validate it personnally. When all coauthors have done it, you can move to the final step.

5. Invitation of readers

In this final step, you invite peers to read your article. The point is that they may turn into reviewers, 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 carefully think about who you want to invite before this final step. Indeed, it is important not to invite only the few best specialists of your field. We remind you that in SJS, articles are not seen as valid because two individuals decided so but because there is an observable community-wide consensus around it. After final validation, the current date will become the publication date on SJS of your article. Later, you can still invite yourself more readers and promote your article as you think fit.

6. Revising an article

The revision process is not yet fully automated. For now, it is only possible with our help. Contact us at support@sjscience.org with object “Revision”.

Personal account

Your personal account has a public and a private view. The public view displays the profile and the 3D scientific activity of the account owner through four tabs, whose titles are self-explanatory : Profile, Articles, Reviews/Discussions/Prioritization, Self-Journal. Only you can access the private view of your account by signing in and clicking "My account" in the top bar. In that case, the tab "Self-Journal" allows you to edit your own self-journal. You also have access to one more tab "Parameters & Following options". This tutorial elaborates on these two latter tabs.

Self-Journal

In public view, this tab allows to browse the issues already published by the account owner. In private view, this tab allows you to privately build the current issue of your self-journal. You can make it public by clicking on “Preview this issue” then on “Release this issue”. The first button becomes active when your current issue has a title, an editorial, at least one keyword and at least 4 articles. You cannot edit an issue after you have published it. Besides your mere selection of articles, the scientific value of your self-journal also lies in your comments, so it is 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 of the article's page.
  • Otherwise, click the “Add external article” button and provide the metadata of the article : its title, its 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), its publication date. There are two other optional fields : the abstract of the article and an abstract graphics (.jpg or .png) to improve the layout of your self-journal. Authors are provided in the following fashion :
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The following item will be created so that you can order and comment 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 the article.

Parameters and following options

This important tab gives you control of a powerful tool to perform an automatical watch of SJS' scientific activity in a highly customized way.
You can follow i) the activity of other members, ii) the activity around given articles, iii) the release of new journal issues and iv) have topical queries automatically launched. You can decide the frequency of reports of activity sent to you by SJS. Importantly, SJS' policy is not to spam its users. We are unfortunately aware that a scientist's mailbox tends to be overloaded by irrelevant information, so we want to guarantee 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. Therefore, you can safely use this powerful tool : you will get nothing else than what you explicitely asked for.
  • In this tab, you can set the frequency at which most recent positive results of your queries are aggregated and reported to you.
  • To follow an article, you must 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 a member or subscribe to his/her journal, you must click on the relevant buttons in his/her account (to the right of his/her picture). This will create an item in the section "Followed articles" or "Subscribed journals". Again, you can select which type of member's activity is reported to you : new articles, prioritizations, reviews, discussions.
  • You can ask SJS to automatically launch queries and report new results. You need to complete a query in the "Search" engine of SJS and click on "Save this query". After naming it, it will appear as an item in the section "Saved search queries". From there, you can i) manually launch this query by clicking on the corresponding item and ii) have SJS automatically launch it by ticking the box "Report new results".

The Tree of Knowledge (ToK)

The Tree of Knowledge is a consensual structured vocabulary that serves to map all scientific activity. When properly tagged with keywords from the ToK, data can be extracted from SJS easily, exhaustively and unambiguously without the interference of artificial intelligence algorithms. There are two types of links between keywords in the ToK : a link "Narrower concepts" (which can be thought as a link father-son) and a link "Related concepts" which connect keywords from distant parts of the ToK (which can be thought as a link "cousin"). These links allow for the logical browsing of the Tree. 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. 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 interface of the ToK

The main interface is accessed by clicking "Tree of Knowledge" in the top bar. This interface allows for the management of keywords and the browsing 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. Those keywords belong to another branch of the ToK while being related to the current keyword.
4) Parents of the current keyword. Click on any of them to go higher into 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 propose a new narrower concept of the current keyword by clicking this button. This new keyword will be open to vote (see 9)
8) After signing in, you can propose a connection between the current keyword and another one which is already present elsewhere in the ToK. Start writing the target keyword and select it in the autocompletion menu, then click “Create link”. This new connection will be open to vote.
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 triggered by the button "Pick keywords", available in different contexts on the website (such as the search engine). This interface allows for the selection of 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, its metrics (1) and allows for its peer review (2). The left sidebar (3) provides an number of aditional features.

Peer review and discussion interface

A + button is attached to each paragraph and figure. It activates the following interface :

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It contains two forums "Reviews" and "Discussions" (1), dedicated to the paragraph or figure. Only signed members can write into these forums. Each forum can host many threads. A new thread can be created by clicking "New thread" (2). A given thread may contain a lot of replies (3); they can be unfolded by clicking "See all replies". You can use mathematical notation by including LaTeX code between two $ (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 at most once. The rationale of these buttons is mainly to highlight the most relevant reviews (to the article's authors and to other readers) and to filter out irrelevant ones. These votes must be used in connection with the possibility to sort posts by date, by vote + and by vote - (7).

General reviews or discussions regarding the article should be posted in the forums attached to its abstract.

Article metrics

There are three important metrics on SJS: validity, priority, scientific value.

The validity is given by a community-wide choice between two possibilities displayed at the top of the article: "The article has reached scientific standard" and "This article still needs revision". When signed in, you can click at most once on one of this button: 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 the "scientific standard". Rather, the scientific standard is dynamically self-defined by the community by stating which articles have reached it and which ones have not.

The priority represents the short-term importance of the article. Clicking on "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 personal journal automatically triggers the prioritization of the article.

The scientific value of the article is caught by its number of editors. It is displayed in the left sidebar. It counts the number of SJS members that have edited the article in at least one of their journal issues.

Left sidebar

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1) Add to my Journal. When logged, this feature creates an item in the Journal tab of your account and prioritizes the article (unless you had already done it).
2) Follow this article. When logged, using this feature creates an item in the Parameters & Following Options tab of your account and prioritizes the article (unless you had already done it).
4) "Reviews and discussions" displays all reviews and discussions posted for this article. It is mainly meant to have a quick overview of the "hot spots" of the article through filtering of comments with + and - minus votes.
5) The outline lets you browse quickly the different sections of the article

FAQ

1) How to follow science on SJS?

Following science means two things:
i) Staying informed of new articles that are relevant to you.
ii) Understanding the different directions and trends in your field.

SJS provides easy, powerful and highly automatized means to follow science exhaustively and with minimal noise. The following points help you to 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 on "Follow XX" on the personal page of a peer and select which aspects of his/her activity you want to follow in your "Parameters and following options".
  • Follow the activity around an article:
  • i) its reviews
    ii) the discussions it triggered.
    iii) its revisions
    Click on "Follow this article" and fine tune your "Parameters and following options".
  • Keep up to date with topics using the SJS' Tree of Knowledge feature:
  • i) Directly access associated articles and scientists
    ii) Set up an alert for keywords in 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' journals and edit your own journal to spread your ideas within your community.
In short :
1) Keep up to date with the activity of peers, articles, topics and journals with the automated means provided by SJS.
2) Check periodically the Tree of Knowledge for new keywords associated with your field(s) of interest.

2) Is SJS' content 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 thing, just trust us". However, consistently 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 e.g. 100Mb of their own hard-disk space to keep 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 us scientists take responsibility, we will do something better and cheaper than any other solution.

There is a free software preparing this move: http://ceph.com . If you have some skills, go and help them! It is working but it is not user-friendly enough yet to install and configure.

3) How to cite an article from SJS?

Authors, title, date, version number, URL.

It is necessary to cite which version you had access to since authors may still modify their article after you have cited it.
If the article has an equivalent version published in an academic journal, please cite it 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 comes from other ways.