Stepping into an area about which I have strong opinions. I appreciate your effort, I just think you're way off base.
Physical Review Letters in journal (aka pdf) format are ideal. Nothing is especially stylish, but it's a simple, easy to read format that highlights figures as a way to convey the meaning of the work. I much prefer the PDF to the online version.
Some critics of your site (all in the spirit of "I hope you take this as a challenge to do better or maybe just realize there's not a lot wrong in the first place"):
-your color contrast hurts my eyes (light grey on blue...)
-the graphs are hard to understand (no axis labels on some, no captions to understand what's going on since that's all most people read first anyways, lack of contrast)
-typeset equations are ugly (can't beat LaTeX)
-drastic font size difference between code and text is jarring
-no authors listed so I can instantly disregard your work because I've learned not to trust your methods (I kid, I kid... kindof)
-the draggable figures did nothing for me
-your column width was too narrow. Aim for 10-14 words per line.
-because I have to scroll it's hard to quickly scan it for parts I actually want to read. When you read 10-20 papers a day, this is important.
One thing I really like: click the Fig. # and it scrolls to be beside the text. That is a nice feature that online journals can learn from.
In short, I think you're trying to solve a non-existent (or at least minimally existent) problem. LaTeX is beautiful, but perhaps you don't appreciate it. Journals in print (except for Science and Nature which blend all their articles together) generally look really nice. The PDF's of individual articles are the thing to read online, and I think your solution is a long way from any sort of reasonable online reading experience.
As a grad student who reads lots of papers (with a typical length of 30+ pages), I too have a strong opinion on this. I think PDFs do not serve the needs of the day and such efforts are a step in the right direction.
PDFs okay if you plan to print out the papers to read and are just about bearable if you read the papers on a large monitor. They are quite unfriendly for tablets or smaller laptops -- starting with the multiple vertical columns, which are taller than the screen height. The font size is dictated by the aim of reducing printing costs rather than reading convenience. Just for starters, a "responsive" reader with the ability to resize fonts would make a big difference. Notes/references which appear on the side (rather than the bottom of the page) or links to interactive data (which scientists will have to figure out a good way of using) would drastically improve the reading experience and the efficacy of this mode of scholarly communication.
One of the downsides to the formats (including PDF) currently used in academia is that their layout and typography is fixed by the author, and optimized for printing. You can't reflow the text for the screen unless you have the original source document.
For example, most papers use multiple columns. This optimizes for readability when printed in A4/Letter, but on a computer screen it's much harder to scan and read pages this way, compared to a strictly linear layout -- especially when the text is interspersed with graphs and tables.
Another example: Paragraphs are usually signaled with a line break and an indent. Papers seldom use any spacing between paragraphs. I think indented paragraphs work well for fiction, less so for academic texts.
The papers mentioned in this thread by dfc are good examples of those two problems.
Your criticisms are of the submission's design, not the idea. I don't think that this submission fully emphasizes the advantages of a dynamic, interactive document as a medium for conveying ideas. I think this does it much, much better:
Having been offered a part-time job to typeset LaTeX, I do really like it :) I used MathJax, which was the best math typesetting I could find for the web.
Without disrespecting your criticisms at all, is there any sort of dynamism which would make you want to read something other than the pdf?
Also as someone who has strong opinions, I concur that PDFs are great, especially for archiving purposes. As a distillation of important information, I think they're ideal.
That said I think we need something else in addition to PDFs, rather than to replace them. Dynamic graphs, for example, and the ability to export raw data. In my field, rotatable/zoomable 3D views for molecules and crystals and the like would be great, as well as being able to measure bond lengths and angles. This would be infinitely superior to a static 2D projection. But these should all be in addition to: I still want a PDF I can take with me and read offline if necessary.
.. and some lines were far too tight and some were far too loose, at least in my browser. I am 54 and I can't see some things that I expect a 24 year old can see, and I depend on interword space to be there.
Slightly off topic, but I wish there was a change to how scientific papers were written (and this comment doesn't pertain to this article - it's just a general comment). For some, inexplicable reason, it sometimes feels like authors are challenging one another to write the most convoluted, unclear account of what is actually a fairly intuitive idea.
Clearly, this is not always the case, and obviously complexity doesn't lend itself to nice 10 word summaries (hat-tip to Jed Bartlet), but equally the choice of language used and the pace of arguments can make a huge difference. There is no need to use "big" words, when simple ones will do just fine. There is no need to use technical language in place of standard vocabulary where it adds nothing to further your ideas. Don't "hit the ground running" but introduce a new idea with an analogy, or a toy example.
Write papers so humans can understand them - often the science being portrayed is complicated enough, there's no need to further complicate your ideas to the point where you leave English speaking audiences trying to decipher the message, let alone what foreign readers must think.
The best papers are the papers you can read abstract-to-conclusion without stopping and asking yourself, "What does that mean?". This is all too rare an occurrence for me. /rant
The fundamental issue is that papers are often incremental, that is, they build upon some previous work, which is thereby referenced. The issue this creates is that the papers become hard to follow for anyone who is not already familiar with the previous work in the cited papers. Even if someone goes on to read the referenced papers, it often does not help as the problem is recursive.
This keeps on happening till the research becomes old and mature enough for someone to write a book on the topic which then is nearly self-contained (or assumes some prior background like mathematics, or undergrad-level courses, etc.). MOOCs are also helping the situation since the instructors create nearly self-contained courses which often also include very recent research results.
To solve the issue you mention, this basic notion may need to be broken, such that each paper explicitly explains its subject matter without relying too much on the references. Since much research does not go anywhere, this may be a premature optimization really though.
A thing that does bother me, and signifies the extent to which what you say is true is that "talking" to the authors of these papers nearly always delivers those good insights within a few minutes that you would not get after spending an hour on the paper they wrote.
Scientific papers aren't written for you, the layman. They are written specifically for scientists in that particular field. I'm a PhD student, and never have I read a paper with wording that I would describe as "convoluted."
A great example of a web-friendly, interactive view of a scientific paper is the eLife Lens, example here: http://lens.elifesciences.org/#00380 . They announced the open source project back in June (blog post http://www.elifesciences.org/lens/). This is the direction that web-based paper views are moving toward, and some publishers (notably PLOS) already have quite nice interactive components.
PubMed, the government-run biomedical abstract database, also recently introduced its PubReader app for reading biomedical papers (http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/). But my money's on eLife here — NCBI is better known for its databases than its user interface design (to say the least).
It would be great to see some innovation here (some publishers have absolutely awful web-based journal article views). But as the main format for paper publishing and dissemination, I think the PDF won't be going away anytime soon.
I really like plos, but one criticism I have of their interface is that the figure takes up the entire page, which destroys my easy reference to the rest of the content. e.g. at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fj... Figure 1 takes up the entire height of my screen on my laptop and then I have to scroll back to where it is in the text.
fwiw I considered using the Strogatz paper as an example for consistency (maybe it could become something of a standard for reimagining paper layouts), and use tangle or knockout, but I decided to get feedback sooner rather than later after reading a line in pg's essay today re: procrastination.
Clicking on a link and having a figure appear solves a small but real problem.
In mathematical papers it'd be nice to be able to do the same with equation references --- click on the equation number, and the equation would magically appear in the margin. Ditto bibliography entries, theorem statements, definitions, and so on. I guess there are possible solutions other than having them appear in the margin, too.
Thanks! I was thinking about doing the same with bib refs since I don't like being sent to the bottom of the page like a footnote. I really like the idea of doing the same thing with theorems, defs, etc.
I'm a bit worried about what to do with column overload, though, if I add a col for X, a col for Y, etc. Perhaps a hover-text is better but that would obscure the content ...
This is quite unreadable with the low contrast colors and the columns are much too small. If you pick a random paper on the arxiv[1] and imagine how much vertical space it will take to just to show the text you'll see the problem.
I think you're right re: contrast, but I'm still conflicted about column size. On the one hand, a wider column gives better justified results, but on the other hand, it makes the sliding figure column more difficult on 13 in. Screens. Which did you find more beneficial, wider columns, or sliding figures?
I came in to mention the tufte latex class. It is unfortunate that you posted the link with no context. If you are going to post a link with no context I would think that one of the two samples would have been a better choice:
"The Tufte-LATEX document classes define a style similar to the style Edward Tufte uses in his books and handouts. Tufte’s style is known for its extensive use of sidenotes, tight integration of graphics with text, and well-set typography. This document aims to be at once a demonstration of the features of the Tufte-LATEX document classes and a style guide to their use."
The layout is nice, but I found the text really difficult to read with the lack of contrast. I imagine it would be next to impossible for someone with a vision impairment.
Thanks. Did you like the auto scrolling of each column depending on what was clicked?
re: contrast, I've found black on white is too harsh for me (I like the 'lights out' setting on project euler for instance.) Do you prefer dark text on light bg, or light text on dark bg?
I don't generally read scientific papers, but I found it annoying that I had to click on the "Figure 1" in the text to see the figure, and that the space in the figure seemed useless until you hit the reference in the text.
Part of me wants parallax scroll, but I'm sure that would be a terrible fit unless you had the right number of diagrams and the references to diagrams were equally spaced out (as opposed to having two in the same line).
This also reminds me of good old <frame>s from the 90s...
Edit: I realized afterwards that you refer to some diagrams multiple times, such as Figure 4. I guess this is a step towards not having to flip back three pages in the PDF to get to that diagram, but I'm not sure it's a "300x improvement" that would cause scientists/academics to switch away from LaTeX (or use your new LaTeX module, if you went that way) any time soon.
I'm not sure what you mean re: click on "Figure 1" to see it. You could scroll back up, but I thought that was the equivalent of flipping back pages. In a lot of scientific papers I read the figure is not on the same page as the first introduction. I considered fixing them to one position, or placing them within the text like most people do, but this interrupted the flow for me.
re: "Edit" It's not a 300x improvement by any means. Definitely less cool than the research I get to do ;) That said, I would like to see things switch away from LaTeX as typesetting gets better on the web. I love LaTeX, and was even offered a part-time gig as a LaTeX editor for an economist that has 3 full-time typesetters (I'm not even kidding, he must take division of labor seriously). But it doesn't seem to allow for the same kind of freedom we have now as a result of newer media: it's optimized for print, even with addons like hypertext.
You should make the source more discoverable, particularly on your 'homepage'.
Particularly on a site like this, but also in general, in doesn't take much more effort to write a pull request than it does to write a comment.
For example, modifying the colour scheme or layout would be a few lines changed in the css. Encourage people to give the most useful feedback they can - patches!
I should probably go and raise a PR implementing this now, but I've already spent so long writing this comment... ;)
[EDIT] Adding a Readme to the repository would help people understand how everything is organised as well (for people who want to look at the nuts and bolts), and a License file would clarify what, if any, modification of your work is allowed.
To use: click 'text' to sync text col to reference of figure in text, multiple times if there are multiple are multiple references, drag a figure, resize a figure, click 'reset', click a figure reference to sync to the figure col.
I know there are a few editors that read this, I would love to see better interfaces for your journals ;).
The justified cols aren't great yet on web browsers and I was getting too much white space. I think I'll go back to left-align given your feedback, thanks. For what it's worth, the extent of my design knowledge is "Design for Hackers" so I don't claim to be an expert or anything.
Odd, it doesn't do that for me on ff22windows. I originally messed with word spacing because it looked too sparse, but I'm going to switch it back to something safer. Thanksforthefeedback;)
[+] [-] rubidium|12 years ago|reply
Physical Review Letters in journal (aka pdf) format are ideal. Nothing is especially stylish, but it's a simple, easy to read format that highlights figures as a way to convey the meaning of the work. I much prefer the PDF to the online version.
Some critics of your site (all in the spirit of "I hope you take this as a challenge to do better or maybe just realize there's not a lot wrong in the first place"): -your color contrast hurts my eyes (light grey on blue...) -the graphs are hard to understand (no axis labels on some, no captions to understand what's going on since that's all most people read first anyways, lack of contrast) -typeset equations are ugly (can't beat LaTeX) -drastic font size difference between code and text is jarring -no authors listed so I can instantly disregard your work because I've learned not to trust your methods (I kid, I kid... kindof) -the draggable figures did nothing for me -your column width was too narrow. Aim for 10-14 words per line. -because I have to scroll it's hard to quickly scan it for parts I actually want to read. When you read 10-20 papers a day, this is important.
One thing I really like: click the Fig. # and it scrolls to be beside the text. That is a nice feature that online journals can learn from.
In short, I think you're trying to solve a non-existent (or at least minimally existent) problem. LaTeX is beautiful, but perhaps you don't appreciate it. Journals in print (except for Science and Nature which blend all their articles together) generally look really nice. The PDF's of individual articles are the thing to read online, and I think your solution is a long way from any sort of reasonable online reading experience.
[+] [-] ssivark|12 years ago|reply
PDFs okay if you plan to print out the papers to read and are just about bearable if you read the papers on a large monitor. They are quite unfriendly for tablets or smaller laptops -- starting with the multiple vertical columns, which are taller than the screen height. The font size is dictated by the aim of reducing printing costs rather than reading convenience. Just for starters, a "responsive" reader with the ability to resize fonts would make a big difference. Notes/references which appear on the side (rather than the bottom of the page) or links to interactive data (which scientists will have to figure out a good way of using) would drastically improve the reading experience and the efficacy of this mode of scholarly communication.
[+] [-] lobster_johnson|12 years ago|reply
For example, most papers use multiple columns. This optimizes for readability when printed in A4/Letter, but on a computer screen it's much harder to scan and read pages this way, compared to a strictly linear layout -- especially when the text is interspersed with graphs and tables.
Another example: Paragraphs are usually signaled with a line break and an indent. Papers seldom use any spacing between paragraphs. I think indented paragraphs work well for fiction, less so for academic texts.
The papers mentioned in this thread by dfc are good examples of those two problems.
[+] [-] conradev|12 years ago|reply
http://worrydream.com/LadderOfAbstraction/
https://news.ycombinator.com/item?id=3099595
see also: Khan Academy
[+] [-] egocodedinsol|12 years ago|reply
Without disrespecting your criticisms at all, is there any sort of dynamism which would make you want to read something other than the pdf?
[+] [-] dfc|12 years ago|reply
http://prl.aps.org/pdf/PRL/v111/i1/e012001
or
http://prl.aps.org/pdf/PRL/v105/i25/e252302
[+] [-] Osmium|12 years ago|reply
That said I think we need something else in addition to PDFs, rather than to replace them. Dynamic graphs, for example, and the ability to export raw data. In my field, rotatable/zoomable 3D views for molecules and crystals and the like would be great, as well as being able to measure bond lengths and angles. This would be infinitely superior to a static 2D projection. But these should all be in addition to: I still want a PDF I can take with me and read offline if necessary.
[+] [-] studentrob|12 years ago|reply
If LaTeX were to add a way to associate figures with text, then someone could write a converter from LaTeX to HTML to implement this idea.
[+] [-] jimhefferon|12 years ago|reply
.. and some lines were far too tight and some were far too loose, at least in my browser. I am 54 and I can't see some things that I expect a 24 year old can see, and I depend on interword space to be there.
[+] [-] alexholehouse|12 years ago|reply
Clearly, this is not always the case, and obviously complexity doesn't lend itself to nice 10 word summaries (hat-tip to Jed Bartlet), but equally the choice of language used and the pace of arguments can make a huge difference. There is no need to use "big" words, when simple ones will do just fine. There is no need to use technical language in place of standard vocabulary where it adds nothing to further your ideas. Don't "hit the ground running" but introduce a new idea with an analogy, or a toy example.
Write papers so humans can understand them - often the science being portrayed is complicated enough, there's no need to further complicate your ideas to the point where you leave English speaking audiences trying to decipher the message, let alone what foreign readers must think.
The best papers are the papers you can read abstract-to-conclusion without stopping and asking yourself, "What does that mean?". This is all too rare an occurrence for me. /rant
[+] [-] alok-g|12 years ago|reply
This keeps on happening till the research becomes old and mature enough for someone to write a book on the topic which then is nearly self-contained (or assumes some prior background like mathematics, or undergrad-level courses, etc.). MOOCs are also helping the situation since the instructors create nearly self-contained courses which often also include very recent research results.
To solve the issue you mention, this basic notion may need to be broken, such that each paper explicitly explains its subject matter without relying too much on the references. Since much research does not go anywhere, this may be a premature optimization really though.
A thing that does bother me, and signifies the extent to which what you say is true is that "talking" to the authors of these papers nearly always delivers those good insights within a few minutes that you would not get after spending an hour on the paper they wrote.
[+] [-] fjdghsd|12 years ago|reply
[+] [-] gjuggler|12 years ago|reply
PubMed, the government-run biomedical abstract database, also recently introduced its PubReader app for reading biomedical papers (http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/). But my money's on eLife here — NCBI is better known for its databases than its user interface design (to say the least).
It would be great to see some innovation here (some publishers have absolutely awful web-based journal article views). But as the main format for paper publishing and dissemination, I think the PDF won't be going away anytime soon.
[+] [-] egocodedinsol|12 years ago|reply
I really like plos, but one criticism I have of their interface is that the figure takes up the entire page, which destroys my easy reference to the rest of the content. e.g. at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fj... Figure 1 takes up the entire height of my screen on my laptop and then I have to scroll back to where it is in the text.
[+] [-] michaelmior|12 years ago|reply
[+] [-] timf|12 years ago|reply
http://worrydream.com/ScientificCommunicationAsSequentialArt...
You can mess with the sliders, etc.
Video @ http://vimeo.com/67076984
[+] [-] egocodedinsol|12 years ago|reply
fwiw I considered using the Strogatz paper as an example for consistency (maybe it could become something of a standard for reimagining paper layouts), and use tangle or knockout, but I decided to get feedback sooner rather than later after reading a line in pg's essay today re: procrastination.
[+] [-] michael_nielsen|12 years ago|reply
Clicking on a link and having a figure appear solves a small but real problem.
In mathematical papers it'd be nice to be able to do the same with equation references --- click on the equation number, and the equation would magically appear in the margin. Ditto bibliography entries, theorem statements, definitions, and so on. I guess there are possible solutions other than having them appear in the margin, too.
[+] [-] egocodedinsol|12 years ago|reply
I'm a bit worried about what to do with column overload, though, if I add a col for X, a col for Y, etc. Perhaps a hover-text is better but that would obscure the content ...
[+] [-] lrem|12 years ago|reply
http://skim-app.sourceforge.net/
If the PDF contains proper links, just CMD-click them to bring up the linked position.
★ - one I use, not authored
[+] [-] freyrs3|12 years ago|reply
[1] http://arxiv.org/list/hep-ex/new
[+] [-] egocodedinsol|12 years ago|reply
[+] [-] zeckalpha|12 years ago|reply
[+] [-] dfc|12 years ago|reply
sample handout: http://mirrors.ctan.org/macros/latex/contrib/tufte-latex/sam...
sample book: http://mirrors.ctan.org/macros/latex/contrib/tufte-latex/sam...
For those looking for some context:
"The Tufte-LATEX document classes define a style similar to the style Edward Tufte uses in his books and handouts. Tufte’s style is known for its extensive use of sidenotes, tight integration of graphics with text, and well-set typography. This document aims to be at once a demonstration of the features of the Tufte-LATEX document classes and a style guide to their use."
[+] [-] davidbanham|12 years ago|reply
[+] [-] egocodedinsol|12 years ago|reply
re: contrast, I've found black on white is too harsh for me (I like the 'lights out' setting on project euler for instance.) Do you prefer dark text on light bg, or light text on dark bg?
[+] [-] cbhl|12 years ago|reply
Part of me wants parallax scroll, but I'm sure that would be a terrible fit unless you had the right number of diagrams and the references to diagrams were equally spaced out (as opposed to having two in the same line).
This also reminds me of good old <frame>s from the 90s...
Edit: I realized afterwards that you refer to some diagrams multiple times, such as Figure 4. I guess this is a step towards not having to flip back three pages in the PDF to get to that diagram, but I'm not sure it's a "300x improvement" that would cause scientists/academics to switch away from LaTeX (or use your new LaTeX module, if you went that way) any time soon.
[+] [-] egocodedinsol|12 years ago|reply
re: "Edit" It's not a 300x improvement by any means. Definitely less cool than the research I get to do ;) That said, I would like to see things switch away from LaTeX as typesetting gets better on the web. I love LaTeX, and was even offered a part-time gig as a LaTeX editor for an economist that has 3 full-time typesetters (I'm not even kidding, he must take division of labor seriously). But it doesn't seem to allow for the same kind of freedom we have now as a result of newer media: it's optimized for print, even with addons like hypertext.
[+] [-] Cogito|12 years ago|reply
Particularly on a site like this, but also in general, in doesn't take much more effort to write a pull request than it does to write a comment.
For example, modifying the colour scheme or layout would be a few lines changed in the css. Encourage people to give the most useful feedback they can - patches!
I should probably go and raise a PR implementing this now, but I've already spent so long writing this comment... ;)
[EDIT] Adding a Readme to the repository would help people understand how everything is organised as well (for people who want to look at the nuts and bolts), and a License file would clarify what, if any, modification of your work is allowed.
[+] [-] egocodedinsol|12 years ago|reply
I'm not sure how much it's a software project so much as a proof of concept. If you did want it to be more of a project, what would you suggest doing?
[+] [-] egocodedinsol|12 years ago|reply
I know there are a few editors that read this, I would love to see better interfaces for your journals ;).
[+] [-] andrewcooke|12 years ago|reply
edit: word-spacing: -2px; wtf?
[+] [-] leephillips|12 years ago|reply
[+] [-] egocodedinsol|12 years ago|reply
[+] [-] kumarski|12 years ago|reply
[+] [-] fmsf|12 years ago|reply
[+] [-] chj|12 years ago|reply
[+] [-] fdej|12 years ago|reply
[+] [-] egocodedinsol|12 years ago|reply
[+] [-] whatsup|12 years ago|reply
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[+] [-] kumarski|12 years ago|reply
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