A few days ago we released the experimental version of Docear and wrote about it in our experimental release forum (you can subscribe to that forum if you want to be informed about new experimental releases). Today we declare Docear 1.01 as stable and from now on it’s available on our primary download page. Changes are rather minor.
- A slightly modified dialog for selecting your PDF viewer (some links were updated)
- The labeling of the file monitoring settings are now more uniform
- The colors for “Move …” in the “Nodes” ribbon were changed from green to blue. There’s quite a funny story behind it. One of our team members recently told me that the arrows for moving nodes would point to the wrong direction. I told him that they were absolutely correct and we had quite a discussion. Then we realized that the team member is (red-green) color blind and couldn’t recognize the green arrows properly. Well, now the arrows are blue (see screenshot) and all people should be able to recognize them correctly
In addition, we did some bug fixes.
Help us to make Docear even better, improve your software development or statistic skills, spend your time in sunny Germany, and get paid for it!
Like the previous years, we offer the opportunity for Bachelor students from the US, UK or Canada to do a paid internship at Docear in summer 2014. The internship should last for 8-12 weeks with the earliest start date being May and the latest being August. You will be paid 650 Euros a month, a 160 Euro allowance for travelling, and health insurance. International travel costs will not be covered. You will be placed with Docear’s core team in Magdeburg, close to Berlin. So, if you love Docear as much as we do, are a passionate software developer or statistician (or want to become one), and are interested to spend your next summer in sunny Germany, read on.
Your project will be to improve Docear’s recommender system. As such, it will be your task to support the Docear team in researching how the interests of Docear’s users can be identified from the data, and how these interests can be matched with research papers. You will do literature research, create new ideas, analyze the users’ data, and implement new recommendation approaches in JAVA. Of course, you don’t have to do all of this alone – you will be closely cooperating with us, the Docear team. Your work will be integrated into Docear and used by thousands of researchers around the world. If you are interested you are also very welcome to write a research paper with us, or, if you home university allows this, use your internship to work on your Bachelor’s thesis. If you have other ideas than improving the recommender system, please let us know. We are open to new ideas and you may do anything you want as long as it will make our users happy.
If you are primarily interested in software developing you should have a profound knowledge of the programming language JAVA. Knowledge in statistics, machine learning, other programming languages (especially C/++ or Python) and/or MySQL, neo4j, Hibernate, Jersey, REST Web Services, Tomcat, and Apache is a plus, but not required. If you are primarily interested in research, i.e. analyzing the data we have, you should have profound knowledge in statistics and in at least one statistic software tool (e.g. SPSS, R, …).
The internship is offered in cooperation with the German Academic Exchange Service (DAAD). Therefore, if you are interested in the scholarship, apply before January 31, 2014. To apply, read the application guidelines, register, log-in, browse DAAD’s internship database, find Docear’s project page, and apply.
Even if you are not eligible to apply, or just not interested, please tell your friends of the internship opportunity. This is really important. Only when a significant number of students applies, DAAD will sponsor the project. Therefore, please promote the internship opportunity as much as you can.
Docear4Word v1.21 is available for download. It fixes a bug that caused problems when you provided a ‘-’ as page number without any numbers.
As you probably know, Docear is free and open source. As you might know as well, we do accept donations. Today, we would like to share some statistics with you about the amount of donations we received. Actually, in the past two years, we received 434 US$ (~340€) from from 33 donators. That’s not a lot, given that Docear has several thousands of active users. However, it’s also no surprise and to be honest, we ourselves hardly ever donate for other software tools, so we cannot blame anyone for not donating to Docear (even if he should heavily use it).
The average donation we received was 13.16$ (median was 10$), the highest donation was 50$, the smallest 1$, standard deviation 11.04$. The following chart shows the individual and cumulated donations. Sometimes, we don’t receive any recommendations for several month, sometimes we get multiple ones within a week or so.
This weekend, I had some spare time and I wondered which was the most popular reference manager (and how Docear is doing in comparison). So, I took a list of reference managers from Wikipedia, and checked some statistics on Alexa, Google Trends, and Google Keyword Planner. Since I had the data anyway, I thought I share it with you . Please note that this is a quick and dirty analysis. I cannot guarantee that there is not one or two reference managers missing (i just took the list from Wikipedia), and, of course, there are many alternatives to Alexa and Google for measuring the popularity of a reference manager.
Time to celebrate
Today, Docear 1.0 (stable) is finally available for Windows, Mac, and Linux to download. It’s been almost two years since we released the first private Alpha of Docear and we are really proud of what we accomplished since then. Docear is better than ever, and in addition to all the enhancements we made during the past years, we completely rewrote the manual with step-by-step instructions including an overview of supported PDF viewers, we changed the homepage, we created a new video, and we made the features & details page much more comprehensive. For those who already use Docear 1.0 RC4, there are not many changes (just a few bug fixes). For new users, we would like to explain what Docear is and what makes it so special.
Docear is a unique solution to academic literature management that helps you to organize, create, and discover academic literature. The three most distinct features of Docear are:
- A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, … and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).
- A ‘literature suite concept’ that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.
- A research paper recommender system that allows you to discover new academic literature.
Aside from Docear’s unique approach, Docear offers many features more. In particular, we would like to point out that Docear is free, open source, not evil, and Docear gives you full control over your data. Docear works with standard PDF annotations, so you can use your favorite PDF viewer. Your reference data is directly stored as BibTeX (a text-based format that can be read by almost any other reference manager). Your drafts and folders are stored in Freeplane’s XML format, again a text-based format that is easy to process and understood by several other applications. And although we offer several online services such as PDF metadata retrieval, backup space, and online viewer, we do not force you to register. You can just install Docear on your computer, without any registration, and use 99% of Docear’s functionality.
But let’s get back to Docear’s unique approach for literature management…
You need to look carefully before you know whether a mushroom is truly enjoyable or whether it will give you a bad stomach. The same may be true for reference managers. Photo: Phototace
At time of writing these lines, there are 31 reference management tools listed on Wikipedia and there are many attempts to identify the best ones, or even the best one (e.g. here, here, here, here, here, here, here, here, … ). Typically, reviewers gather a list of features and analyze which reference managers offer most of these features, and hence are the best ones. Unfortunately, each reviewer has its own preferences about which features are important, and so have you: Are many export formats more important than a mobile version? Is it more important to have metadata extraction for PDF files than an import for bibliographic data from academic search engines? Would a thorough manual be more important than free support? How important is a large number of citation styles? Do you need a Search & Replace function? Do you want to create synonyms for term lists (whatever that means)? …?
Let’s face the truth: it’s impossible to determine which of the hundred potential features you really need.
So how can you find the best reference manager? Recently we had an ironic look at the question what the best reference managers are. Today we want to have a more serious analysis, and propose to first identify the bad reference managers, instead of looking for the very best ones. Then, if the bad references managers are found, it should be easier to identify the best one(s) from the few remaining.
What makes a bad – or evil – reference manager? We believe that there are three no-go ‘features’ that make a reference manager so bad (i.e. so harming in the long run) that you should not use it, even if it possesses all the other features you might need.
1. A “lock-in feature” that prevents you from ever switching to a competitor tool
A reference manager might offer exactly the features you need, but how about in a few years? Maybe your needs are changing, other reference managers are just becoming better than your current tool, or your boss is telling you that you have to use a specific tool. In this case it is crucial that your current reference manager doesn’t lock you in and allows switching to your new favorite reference managers. Otherwise, you will have a serious problem. You might have had the perfect reference manager for the past one or two years. But then you are bound to the now not-so-perfect tool for the rest of your academic life. To being able to switch to another reference manager, your reference manager should be offering at least one of the following three functions (ideally the first one).
- Your data should be stored in a standard format that other reference managers can read
- Your reference manager should be able to export your data in a standard format
- Your reference manager allows direct access to your data, so other developers can write import filters for it.
Today we released Docear4Word 1.2. It contains a few bug fixes. More precisely, we upgraded to the latest citeproc-js version which should fix some ordering problems. In addition, there was a bug that prevented to add the issue number of a reference into the bibliography. That is fixed now. Here is the detailed change log:
- CiteProcRunner gets citeproc.js version on first use
- Added Null checks for <field>.Code.Text to ContainsBibliography, EnumerateCSLFields, IsDocearField, IsCitationField, IsBibliographyField
- AboutForm now displays the citeproc.js version number
- Updated citeproc.js to 1.0.474 which fixes some major integration issues
- Issue and Number Tags: If only one present in BibTex then is propagated to both Issue and Number in CSL
In the past, there was a bit of criticism on our teaser video. For many people, it did not really help to understand the main ideas of Docear. Others were complaining about the “annoying” background music. Well, in the past week we created a new video.
For the best viewing experience watch the video in HD directly on Vimeo. Watch it in full-screen but do not upscale it (you can disable scaling in the top-right corner, after switching to full-screen).
We hope that the video illustrates the ideas behind Docear more comprehensively than the previous video. Unfortunately, no one in our team is a native English speaker. So, right now, I had to narrate the video with my great German accent (and yes, I know, my voice is maybe not the most beautiful one to narrate a video). Of course, we would prefer to have the video narrated by a native English speaker. Therefore, our question to all the English Docear users out there: Would you be interested in narrating the video? All you would have to do is to listen to the video, and re-record what I am saying in the video (feel free to correct any grammar errors and rephrase the script, when necessary). If you are interested in doing the narration, please send an email to info A/T docear.org. We could send you the raw video file (created with Camtasia) or you could just record the narration and send us the wav or mp3 file, and we will add it to the video.
And a general question to all of you: How do you like the video? Are there any parts that you don’t understand? Parts that are too long? Do you like the background music? If not, do you have specific suggestions for better music?…?
Finally, we have another question to all the HTML/CSS gurus out there. We are not satisfied with the way the current video is embedded into our website. We would love to have it the following way. On our homepage should be a small thumbnail of the video (it could be a simple image, or the ‘truly’ embedded video). However, when a visitor clicks on that thumbnail…
Thumbnail on our homepage
… the video should open in a new layer that expands to the entire screen but should not become larger than the maximum video size (i.e. 1184 x 666 pixels). I have tried several WordPress plugins, tried to code something myself, but nothing worked. Can anybody help us with this, and either point us to an appropriate WordPress plugin, or tell us which HTML/CSS code to use?
Expanded video in full resolution taking the entire screen
Update: We found a narrator
The 17th International Conference on Digital Libraries (TPDL2013) is almost over. There were many interesting presentations, great weather, and awesome food . I took some pictures, that you also find on Facebook, G+, or as a single file download on Dropbox.
Selecting the appropriate tool (i.e. evaluation method) to measure recommender system quality is crucial (Photo: photocase)
Yesterday, we published a pre-print on the shortcomings of current research paper recommender system evaluations. One of the findings was that results of offline and online experiments sometimes contradict each other. We did a more detailed analysis on this issue and wrote a new paper about it. More specifically, we conducted a comprehensive evaluation of a set of algorithms using (a) an offline evaluation and (b) an online evaluation. Results of the two evaluation methods were compared to determine whether and when results of the two methods contradicted each other. Subsequently, we discuss differences and validity of evaluation methods focusing on research paper recommender systems. The goal was to identify which of the evaluation methods were most authoritative, or, if some methods are unsuitable in general. By ‘authoritative’, we mean which evaluation method one should trust when results of different methods contradict each other.
Our current results cast doubt on the meaningfulness of offline evaluations. We showed that offline evaluations could often not predict results of online experiments (measured by click-through rate – CTR) and we identified two possible reasons.
The first reason for the lacking predictive power of offline evaluations is the ignorance of human factors. These factors may strongly influence whether users are satisfied with recommendations, regardless of the recommendation’s relevance. We argue that it probably will never be possible to determine when and how influential human factors are in practice. Thus, it is impossible to determine when offline evaluations have predictive power and when they do not. Assuming that the only purpose of offline evaluations is to predict results in real-world settings, the plausible consequence is to abandon offline evaluations entirely.
Recommender systems are highly useful. But which ones are best? (Photo: Photocase)
As you might now, Docear has a recommender system for research papers, and we are putting a lot of effort in the improvement of the system. Actually, the development of the recommender system is part of my PhD research. When I began my work on the recommender system, some years ago, I became quite frustrated because there were so many different approaches for recommending research papers, but I had no clue which one would be most promising for Docear. I read many many papers (far more than 100), and although there were many interesting ideas presented in the papers, the evaluations… well, most of them sucked. Consequently, I did just not know which approaches to use in Docear.
Meanwhile, we reviewed all these papers more carefully and analyzed how exactly authors conducted their evaluations. More precisely, we analyzed the papers for the following questions.
- To what extent do authors perform user studies, online evaluations, and offline evaluations?
- How many participants do user studies have?
- Against which baselines are approaches compared?
- Do authors provide information about algorithm’s runtime and computational complexity?
- Which metrics are used for algorithm evaluation, and do different metrics provide similar rankings of the algorithms?
- Which datasets are used for offline evaluations
- Are results comparable among different evaluations based on different datasets?
- How consistent are online and offline evaluations? Do they provide the same, or at least similar, rankings of the evaluated approaches?
- Do authors provide sufficient information to re-implement their algorithms or replicate their experiments?
Today we released the 4th release candidate version of Docear. With all the changes introduced into Docear with RC3, there were still some bugs to fix which could cause some distortion in the workspace tree or even prevented users with Chinese language settings from seeing Docear’s ribbon. RC4 is something like the final touch to our previous version and we really want to keep it save. So, if you want to help us, please download this version of Docear and report any bugs or issues you can find here.
By the way, have you ever wondered if there was an easy way to get rid of all the information you don’t need when you are drafting your papers or organizing your literature in Docear’s mind maps?
You can easily maximize your mind map view by pressing the <TAB> key on your keyboard:
We are currently working on a manual and some additional tutorial videos to make working with Docear a piece of cake for everyone out there.
If you are interested in what we are currently working on, or if you want to view our source code, please have a look at our GitHub repository.
Download (It’s still an experimental version. Do not use it for productive work. Or make backups regularly!!!)
Linux (Ubuntu, Debian, SuSE, Red Hat, …)
All OS (all other operating systems supporting Java 1.6 or higher)
Today we released RC3 (Release Candidate) of Docear 1.0 (not yet on the official download page but here in the Blog only). It has one major change compared to previous Docear versions, namely we got rid of the “Incoming” mind map. In the past, most users never really got used to the idea why there was an ‘Incoming’ mind map and a ‘Literature & Annotations’ mind map. Now, there is only the ‘Literature & Annotations’ mind map but it has a special “incoming” node in which new PDFs are added. We hope that this concept is easier to understand. It also means that when you move a PDF from the incoming node to any other node in the mind map, and you create new annotations in the PDF, the new annotations are directly added to the PDF node in the mind map and there won’t be any new node in the incoming node. However, if you prefer the old concept, don’t worry. You can keep your old incoming mind map and use Docear as you were used to be.
Update 2013-10-14: For a more serious analysis read What makes a bad reference manager?
<irony>Have you ever wondered what the best reference management software is? Well, today I found the answer on RefWorks’ web site: The best reference manager is RefWorks! Look at the picture below. The picture might be a little bit confusing but we did the math: Refworks is best and beats EndNote, EndNote Web, Reference Manager, Zotero, and Mendeley in virtually all categories.
A few months ago we released Docear4Word. Docear4Word is an add-on for Microsoft Word that allows you to insert and format citations and bibliographies very easily in MS Word. Many of our users love Docear4Word. However, not all of our users are using Microsoft Word but many are using OpenOffice or LibreOffice. One of them is Stephen from Uberstudent which is a Linux distribution for learners. Stephen, as many others, urged us to develop an add-on, comparable to Docear4Word, for Libre of OpenOffice. Unfortunately, we don’t have the expertise to do this.
Therefore, we would like you to help us. Do you have experience in developing add-ons for LibreOffice and/or OpenOffice? Then, please contact us. We have prepared a description of what Docear4Libre/OpenOffice should be able to do. Read it carefully, and tell us how long you would need to implement it. And don’t forget to tell us how much money you would want for it. Exactly, we are not expecting you to do it for free. We would be willing to pay something for it. Once we found an appropriate developer we will ask our users to donate for Docear4Libre/OpenOffice and give a good amount ourselves. Also Stephen will ask the users from Uberstudent to donate.
There is a new version of Docear available for download. It’s basically the (experimental) RC1 version done right. RC2 fixes a lot of bugs that were caused by the new workspace model with multiple projects, it features a refined and polished version of the Ribbon, fixes a lot of bugs in general and supports the standard PDF viewers of MacOSX (Preview and Skim) and probably a lot of other viewers as well!
If you are still using Beta9 of Docear, a lot of things will change and improve with this new version of Docear. However converting your old maps to this new format is a one-way process (you can’t use these files with Beta9 of Docear anymore) and the process itself might take some time, depending on the size of your mind maps. Please backup your files before upgrading to Docear RC2.
Some of Docear’s new icons in the ribbon bar
Since March, Docear offers a simple web-based mind map viewer, developed with some of our volunteering students. On next Friday, July 12th, at 10:30am the students will present their final work at the HTW in Berlin. You are sincerely invited to join the presentation and be first to see Docear’s new collaboration and synchronization feature. The work is not yet ready to be released to the public but we hope to completely finish the work in the next few months. However, even the preview is really amazing! Compared to the current online viewer the new “Docear Web” offers lots of features. First of all, you can edit your mind maps online and not only on your own but together with your colleagues. The collaboration works both with your local desktop Docear and with your web-based Docear. That means, you can just start Docear Desktop as you are used to and colleagues of you may work on the same mind maps you are editing either on the Web or with Docear Desktop as well. Collaboration is in real-time, similarly to Google Docs. In addition, there is a Dropbox-like utility that synchronizes all your data between different devices (and the Web). As said, not everything is already fully functional but the preview version has at least all the basic features and gives you a very good idea what to expect for the final version.
Dr. Georgia M. Kapitsaki
Yesterday we welcomed Dr. Georgia M. Kapitsaki here in our main office in Magdeburg, Germany. Georgia is from the University of Cyprus and will stay one month with us. Her main interest lies in our research paper recommender system and she will support us in improving our recommender system and performing some research. We are really excited to have her with us and are grateful to Erasmus who is supporting her stay. If you would be interested in visiting us and working or researching on Docear, let us know. We have many interesting projects to work on :-).
Georgia is also giving some lectures at Otto-von-Guericke University in Magdeburg. The first lecture about model-driven engineering was already yesterday but you could still join her lecture about open source licencing (Wednesday, 1pm, Building 10, Room 111) and privacy protection in ubiquitous computing (Thursday, 1pm, Building 29, Room 301).