Docear4LibreOffice / Docear4OpenOffice: Call for Donation (2500$)

–> Read here for the latest update <–

One of our users’ most requested feature is an add-on for LibreOffice and OpenOffice, similar to Docear4Word, which allows adding formatted references and bibliographies in Microsoft Word based on Docear’s BibTeX files. Unfortunately, we have no skills in developing add-ons for Libre or OpenOffice, which is why we were looking for a freelancer to help us. Now, finally, we found one. The freelancer is offering to develop a pendant to Docear4Word that works with LibreOffice and OpenOffice. This means, you will be able to select a reference from Docears’ BibTeX database, and the add-on will insert the in-text citation and the bibliography in your Libre/OpenOffice document. Analog to Docear4Word, you will be able to choose from more than 2,000 citation styles to format your references.

However, the freelancer is not developing the add-on for free. He asks for 2500 US$ (~1,900€), which we believe to be a fair price. Therefore, we kindly ask you to donate, so we can pay the freelancer to develop a Docear4Libre/OpenOffice. Of course, the add-on will be open-source, reading not only Docear’s BibTeX files but also BibTeX files of other BibTeX based reference managers. The freelancer already developed a simple proof-of concept (see screenshot), which uses citeproc-java to add BibTeX based references. As such, we have no doubts that the freelancer will be able to deliver the promised add-on — if we can collect enough money.

The freelancer’s is already working on the add-on and his goal is to finish it in the next two months or so. However, as long as we cannot pay him, he will not release the add-on, even if he has finished his work (and if he learns that there are no donations coming, he might decide to stop his work at any time). Therefore, if you want a Docear4Libre/OpenOffice, please donate now! Donate 1$, 5$, 10$, 50$ or 500$ — any contribution matters, and the sooner we have all the money, the sooner you can manage your BibTeX references in LibreOffice and OpenOffice.

Donate via PayPal, or, to save PayPal fees, make a SEPA bank transfer to Docear, IBAN DE18700222000020015578, BIC FDDODEMMXXX. SEPA bank transfers are free of charge within the European Union.

 

 

 

 

 


We will keep you posted on the amount of donations, and any important news.
Read more…

Visit Docear at “CeBIT 2014”

On March 10th and March 11th we will be presenting Docear at CeBIT. CeBIT is the digital industry’s biggest and most international event and always worth a visit. We will be at HALL 9, STAND B18. Feel free to visit us and meet the Docear team in person (Stefan will be there, and maybe Joeran).

Docear 1.0.3 Beta: rate recommendation, new web interface, bug fixes, …

Update: February 18, 2014: No bugs were reported, as such we declare Docear 1.03 as stable. It can be downloaded on the normal download page.


With Docear 1.0.3 beta we have improved PDF handling, provided some help for new users and enhanced the way how you can access your mind maps online.

PDF Handling

We fixed several minor bugs with regard to PDF handling. In previous versions of Docear, nested PDF bookmarks were imported twice when you drag & dropped a PDF file to the mind map. Renaming PDF files from within Docear changed the file links in your mind maps but did not change them in your BibTeX file. Both issues are fixed now. To rename a PDF file from within Docear you just have to right-click it in Docear’s workspace panel on the left hand side and it is important that the mind maps you have linked the file in, are opened. We know, this is still not ideal, and will improve this in future versions of Docear.

Rate Your Recommendations

You already know about our recommender system for academic literature. If you want to help us improving it, you can now rate how good a specific set of recommendations reflects your personal field of interest. Btw. it would be nice if you do not rate a set of recommendations negatively only because it contains some recommendations you received previously. Currently, we have no mechanism to detect duplicate recommendations.

rate a literature recommendation set

Read more…

Docear 2013 in review and our plans for 2014

It’s almost a bit late to review 2013 but better late than never. 2013 doubtlessly was the most active and most successful year for Docear, so far. First and foremost, we finally released Docear 1.0, after releasing many Beta and Release Candidates. Of course, Docear 1.0 is far from being perfect, but we are really proud of it and we think it’s an awesome piece of software to manage references, PDFs, and much more. But there were many noteworthy events more, some of which we took pictures of:

We presented several research papers at the JCDL in Chicago, TPDL on Malta, and RecSys/RepSys in Hong Kong. It is always a pleasure to attend such conferences. Not only because they take place at really nice locations, but because you meet really interesting people (for instance Kris Jack from Mendeley, a really enthusiastic and smart guy who develops Mendeley’s recommender system, or Joseph A. Konstan, who is a true pioneer in the field of recommender systems).

2013-09-23_15-08-37--2013_in_review__Docear-reference mananagement

TPDL on Malta

2013-07-18_11-01-10--2013_in_review__Docear-reference mananagement

JCDL in Chicago

2013 hong kong

RecSys in Hong Kong

Almost every year, our mentor Prof. Andreas Nürnberger is inviting his team members to a sailing turn, and so he did 2013. For several days we were sailing the Baltic Sea, learned a lot about team work and had a lot of fun.

2013-08-13_16-25-30--2013_in_review__Docear-reference mananagement

Sailing turn with our mentor Prof. Nürnberger, the Docear team, and some PhD students of his working group

We had the honour to supervise an excellent student team at HTW Berlin thanks to Prof. Weber-Wulff. The students did a great job in developing the Docear Web prototype. It’s a pity that the prototype has not yet found its way into our live system, but we have not had the time to give the prototype the last bug fixes and features it needs. However, this is very high on our todo list.

2013-07-12_15-09-14--2013_in_review__Docear-reference mananagement

Four of the five students at HTW Berlin who developed a prototype of “Docear Web”

Docear is primarily located in Magdeburg, Germany, which is close to Berlin. Therefore, we didn’t think twice when Researchgate hosted the 10th “Recommender Stammtisch” (regulars’ table) in Berlin. There, we could listened to an enlightening talk of Andreas Lommatzsch, and an entertaining introduction of Researchgate’s CEO Ijad Madisch.

2013-11-14_21-09-31--2013_in_review__Docear-reference mananagement

Read more…

Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear

Which one is the best reference management software? That’s a question any student or researcher should think about quite carefully, because choosing the best reference manager may save lots of time and increase the quality of your work significantly. So, which reference manager is best? Zotero? Mendeley? Docear? …? The answer is: “It depends”, because different people have different needs. Actually, there is no such thing as the ‘best’ reference manager but only the reference manager that is best for you (even though some developers seem to believe that their tool is the only truly perfect one).

In this Blog-post, we compare Zotero, Mendeley, and Docear and we hope that the comparison helps you to decide which of the reference managers is best for you. Of course, there are many other reference managers. Hopefully, we can include them in the comparison some day, but for now we only have time to compare the three. We really tried to do a fair comparison, based on a list of criteria that we consider important for reference management software. Of course, the criteria are subjectively selected, as are all criteria by all reviewers, and you might not agree with all of them. However, even if you disagree with our evaluation, you might find at least some new and interesting aspects as to evaluate reference management tools. You are very welcome to share your constructive criticism in the comments, as well as links to other reviews. In addition, it should be obvious that we – the developers of Docear – are somewhat biased. However, this comparison is most certainly more objective than those that Mendeley and other reference managers did ;-).

Please note that we only compared about 50 high-level features and used a simple rating scheme in the summary table. Of course, a more comprehensive list of features and a more sophisticated rating scheme would have been nice, but this would have been too time consuming. So, consider this review as a rough guideline. If you feel that one of the mentioned features is particularly important to you, install the tools yourself, compare the features, and share your insights in the comments! Most importantly, please let us know when something we wrote is not correct. All reviewed reference tools offer lots of functions, and it might be that we missed one during our review.

Please note that the developers of all three tools constantly improve their tools and add new features. Therefore, the table might be not perfectly up-to-date. In addition, it’s difficult to rate a particular functionality with only one out of three possible ratings (yes; no; partly). Therefore, we highly suggest to read the detailed review, which explains the rationale behind the ratings.

The  table above provides an overview of how Zotero, Mendeley, and Docear support you in various tasks, how open and free they are, etc. Details on the features and ratings are provided in the following sections. As already mentioned, if you notice a mistake in the evaluation (e.g. missed a key feature), please let us know in the comments.

Overview

If you don’t want to read a lot, just jump to the summary

We believe that a reference manager should offer more features than simple reference management. It should support you in (1) finding literature, (2) organizing and annotating literature, (3) drafting your papers, theses, books, assignments, etc., (4) managing your references (of course), and (5) writing your papers, theses, etc. Additionally, many – but not all – students and researchers might be interested in (6) socializing and collaboration, (7) note, task, and general information management, and (8) file management. Finally, we think it is important that a reference manager (9) is available for the major operating systems, (10) has an information management approach you like (tables, social tags, search, …), and (11) is open, free, and sustainable (see also What makes a bad reference manager).

Read more…

Docear4Word 1.23 Released

Docear4Word LogoThe new Docear4Word v1.23 is out as Beta version. Changes are

  1. A more detailed error message when there is a parsing error in your BibTeX file.
  2. The latest v1.0.517 version of CiteProc-JS has been included. This should finally solve all the sorting and numbering issues.
  3. We made some adjustment that could improve the performance of Docear4Word. Not sure though, if it will really do.
  4. Special characters such as . ! ? _ ^< > are now allowed in the beginning of a BibTeX name.

Please note that this is probably the last version that is compiled with VS2010 (requiring you to install .NET 2.0). The next release will be compiled with VS2013 (.NET 4) which should solve some compatibility issues with Windows 8.

We have not yet thoroughly tested the new version. So, if you want to be sure to get a stable version wait a few days (if you don’t see any updates here in the next days, users didn’t report any bugs and the current version is stable).

Download Docear4Word 1.23 Beta

Do a paid internship abroad at SciPlore – Summer 2014

The SciPlore team at Google HQ in Mountain View, CA

The SciPlore team at Google HQ in Mountain View, CA

Our partnering research group SciPlore, from which Docear evolved, in cooperation with the German Academic Exchange Service (DAAD) is offering a paid internship for a Bachelor student in the field of computer science. Prerequisite for applying is that you are a student studying at a German university (if you are from the US, UK, or Canada, read here). More details on prerequisites here.

SciPlore is an international team of researchers affiliated with the University of Magdeburg in Germany and  the University of California, Berkeley. As an intern, you will have the chance to spend 6-12 weeks abroad at a research institute collaborating with the SciPlore research team.
SciPlore researches novel approaches in citation and semantic text analysis for quantifying similarities between scientific articles. Similarity assessments are crucial to many Information Retrieval (IR) tasks, such as clustering of documents, recommending academic literature, or automatically detecting plagiarism.

Read more…

Developer for Docear4Word (Mac) wanted

Since more than one year we are offering Docear4Word, an add-in for Microsoft Word that helps you creating bibliographies. Unfortunately, the add-in is only available for the Windows version of Microsoft Word. We would love to offer a Mac Version, too, but don’t have the skills to do this. If you know how to develop add-ons for MS Word on Mac please contact us at info@docear.org. The add-on should be an exact copy of  Docear4Word (Windows) and you could use Docear4Word’s source code as “inspiration”. You wouldn’t have to do this for free, we would be able to pay some money, and I am confident that our users would also donate a significant amount! Just let us know how long it would take you to  implement this add-on and how much you would want for it.

Elsevier (i.e. the owner of Mendeley) “asks” the users of Academia.edu (i.e. a competitor of Mendeley) to take their papers down

A week ago, Elsevier sent messages to some users of Academia.edu, a social network for researchers (Source: Chronicle). Elsevier asked these users to remove some of their papers from their profile page at Academia.edu. Apparently, Elsevier wasn’t happy that the authors published papers that Elsevier holds the publishing rights for. It’s an interesting discussion whether Elsevier has the right to prohibit uploading papers on Academia’s profile page, because authors have the right to publish their articles on their private homepages. Now, authors might argue that their Academia.edu profile is their private homepage.

What is even more interesting is the fact that it’s Elsevier who did this. That is the same company that recently bought the reference manger Mendeley, which, coincidentally, also offers a social network and hence is a competitor of Academia.edu. I wonder, if Elsevier will soon start to send messages to Mendeley users telling them, too, to not  upload their papers to their profile pages. Or, if Elsevier will just send these messages to users of social networks such as Academia.edu and Researchgate to strenghten their own product Mendeley. Either way, it’s not a nice move from Elsevier and confirms the negative attitude that many researchers have against this publisher and it brings back the doubt about Mendeley’s openness.

Some more detailed discussions on this topic can be found here:

Read more…

Docear 1.02 Beta: Serious PDF Bug Fix; added a donation button

We discovered a serious bug in Docear that relates to the PDF management. In some situations, it could happen that when you edited a PDF, the annotation IDs were not recognized correctly, and a conflict was shown. We fixed this bug and publish Docear 1.02 as a beta version today. Right now, the Beta version download is only available in our forum. We would appreciate if you could test the new version. If there are no more serious bugs found, we will publish it as stable version without any further notifications.

We also added a “Please Donate” note to the workspace panel. It leads you to our donation page and you are sincerely invited to make use of that page :-). If you have already donated, if you just don’t want to donate, or if you need every pixel in the workspace, do a right-click on that note and you will be able to hide it. In addition, we also changed the welcome page that opens after you have installed Docear.

New “Please donate” note in Docear

New “Welcome” page 

Read more…

Donation volume rapidly increased during the past 2 weeks


After reporting about the rather low donation volume a few weeks ago, donations rapidly increased during the past two weeks. In these two weeks we received more than 200 Dollars, which is half of what we got in the past two years. We don’t know whether this is caused by Christmas, or by whatever other reasons, but we would like to thank all donators, sincerely. Your donations significantly help to improve Docear!

 

Docear 1.01 with some minor improvements and bug fixes

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. 

Enhancements include

  • 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.

Read more…

Do a paid internship at Docear in Germany, summer 2014 (US, UK, and CA Bachelor students only)

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 (if you are from Germany, please read here). 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.
Here are some of the ideas

Academic Recommender System
Brief Description: One of our main goals is recommending relevant papers, journals, conferences, universities, etc. to our users. To give relevant recommendations we need detailed user models and there are various approaches to do so (content based and collaborative filtering). However, classic user modeling approaches usually focus on modeling interests based on websites, emails, etc. but not on mind maps as Docear is using them. Therefore, it will be your task to find out which existing user modeling approaches are most suitable for mind maps and how they need to be adjusted to be most effective.

This project is a major project which will require lots of time. If you want to do this project as part of an internship of Bachelor/Master thesis, we may break it down to smaller parts. For instance,

You could focus on applying standard user modeling approaches to mind maps. These would be used as a base-line to evaluate the effectiveness of the following approaches
You could focus on the suitability of the terms in a mind map for building a user model and matching them with items (e.g. academic articles)
You could focus on the links and citations in a mind map for building a user model and matching them with items (e.g. academic articles)
You could focus on collaborative filtering, i.e. determining similar users, and recommending items of these similar users
You could focus on combining the previous approaches (of course only after they are implemented)
Expected Results: A Java library that creates user models based on mind maps and matches the user models with appropriate items to recommend.

Expected Research Results (optional): Evaluation of how effective your user modeling library works, based on click through rates or a user study.

Required Knowledge: Java, Databases (MySQL and ideally Neo4j), Text Mining and Information Retrieval (recommended), Machine Learning (recommended), User Modeling (recommended)

Mind Map Analysis (Pure research project)
Description: Mind maps apparently differ in their structure and way of creation from emails, academic papers, or web pages. But what exactly are the differences? Your task will be to analyse the thousands of mind maps we collected from our users and to find out what makes them unique. To do so, you will, among others, compare mind maps with web pages and academic articles (it will be up to you to which other documents you compare mind maps with and where to get these other documents from). Your work will be the ground work for our academic recommender system (see above) because to provide good mind-map based recommendations you need to know the unique features of mind maps.

Expected Research Results: A study about the unique features of mind maps, compared to web pages, academic articles, and maybe emails, social tags and search queries.

Required Knowledge: A programming language to analyse the data (preferably Java, C/++, or Python), XML, some MySQL and ideally Neo4j

Usability Enhancement
Description: Docear is a great software with lots of unique features but to be honest, it’s not very user friendly. Your task is to improve the usability experience of Docear. Find out what disturbs the users and how to make features more accessable and easier to use.

Expected Results: A new version of Docear that is easier to use than the current version

Expected Research Results (optional): A study to find out how much better your new version exactly is. You could either perform a user study (e.g. give certain tasks to users and analyse how long they need for it) or analyse the usage behavior (we monitor which functions users use how often and how long) and find out whether users of your new version use more feature (or need less time to do certain tasks).

Required Knowledge: Excellent Java skills, knowledge in user interface design, OSGi (recommended) and it would certainly help if you had used Docear for a while to know the workflow.

Searching and filtering via 2-dimensional tags (i.e. attributes): One of Docear’s most powerful features

One of Docear’s most unique feature is its “single-section” user-interface, which allows a highly effective organization of your PDFs, references, and notes. When you want to look-up some information you browse through your data, and usually you should be able to find what you are looking for quite fast. However, sometimes browsing your data is not ideal and you want to search over the papers’ full-text or meta data (title, author, …), or you want to use (social) tags to classify your papers.

Unfortunately, there is one problem about tags: they are one-dimensional. Imagine, you wanted to do a literature survey about recommender systems, and you have dozens of papers about this topic. Some of the papers’ authors evaluated their recommender system with user studies, some with offline experiments, and some with online experiments. The user studies were conducted with with different amounts of participants e.g. one study was conducted with 20 participants, one with 43, and one with 68. With social tags it would be difficult to represent this information. Of course, you could easily add the tag “recommender system” to each of your papers, but how about reflecting the evaluation type? Would you want to create different tags for each evaluation type, i.e. evaluation_user-study, evaluation_offline, evaluation_online? You might do this, but in situations with more than three options this approach would become confusing. You definitely run into a problem when you want to store the amount of study participants via social tags. This simply wouldn’t be possible except maybe you would create tags like no_of_participants_1-10, no_of_participants_11-50, etc.

What you would want to have are “2-dimensional” tags, i.e. one dimension for adding e.g. the tag “evaluation_type” to a paper and one dimension for specifying which evaluation type it is (e.g. “offline evaluation”). In Docear, there are two-dimensional tags, i.e. attribute-value pairs, and these attributes give you much more power than social tags. Here is, how it works:

Read more…

Docear4Word 1.21 with a small bug fix

Docear4Word LogoDocear4Word v1.21 is available for download. It fixes a bug that caused problems when you provided a ‘-‘ as page number without any numbers.

Docear’s users donate $434 in two years (i.e. ~4 Cent per user)

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.

Read more…

On the popularity of reference managers, and their rise and fall

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.

Read more…

Docear 1.0 (stable), a new video, new manual, new homepage, new details page, …

Today, Docear 1.0 (stable) is finally available for Windows, Mac, and Linux to ico16download. 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:

  1. 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).
  2. 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.
  3. 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…

Read more…