Mendeley, Sente, or Papers? No, Zotero and iAnnotate will do.

This is a nerdy blog post, relevant only for researchers.

Every researcher needs to read academic papers. I often do this while commuting or being away from office. It often happens that I don't have a hard copy of the paper that I want to read while being away from office. I never know which paper I want to read in advance.

With the advent of iPad, this problem can be solved by storing all the academic papers in iPad. But that's not the end of the solution. Two more things need to be solved: annotation and bibliography management.

I often highlight some sentences in an academic paper. I also often add a note to the paper. I even sometimes draw a simple graph on the paper. This needs to be done on the iPad screen.

Plus, I need to manage bibliography. Currently, I'm using Zotero for bibliography management, but this Firefox plugin doesn't allow me to read a PDF file with the annotation function. Ideally, every time I download a PDF copy of an academic paper onto iPad, a new entry should automatically be created in this bibliography. Then it's going to be easy to create the section of references in my own paper, in my lecture syllabus, or in an email message that I write to refer my colleagues to the papers they might be interested in.

It seems there is no perfect solution for all these. Partial solutions are provided by Sente, Papers, Mendeley, and iAnnotate.

If I don't need to use an iPad (which is totally out of question but...), Mendeley is the best solution because you can automatically sync with Zotero, which is still the best solution to easily create bibliography while downloading a PDF file of the paper. After visiting the webpage of an academic paper in Firefox, click the reference icon that shows up on the address bar of the Firefox, and then bibliography information will be stored to Zotero and thus to Mendeley. Then download a PDF file from the same webpage to a folder on my desktop computer and drag the icon to Mendeley window. This allows me to read the PDF file on Mendeley, which allows me to annotate.

The problem with Mendeley is that its iPad application does not allow you to annotate. How stupid it is.

Annotation on iPad is not a problem with Sente or Papers. But both are rather poorly designed in terms of the automatic bibliography entry creation while downloading a PDF file of the academic paper. Plus, Sente's annotation function is stupid in the sense that you cannot associate your note to a particular sentence that's highlighted. Notes are only associated with a page.

In terms of annotation on iPad, iAnnotate seems to be the best application. However, it doesn't come with the bibliographic management function. An ideal solution is to combine iAnnotate with Mendeley, but Mendeley does not allow you to read the PDF file annotated with iAnnotate.

What makes things worse is that any of these iPad applications (Sente, Papers, and iAnnotate) is not free. There's even no trial version. Each costs less than 10 US dollars, but should I buy all of these to test which is the best among available?

It seems that's the way to go in the world of Apps. Buy several alternative applications for your iPad (or iPhone) and choose the best....


UPDATE:
It seems the quick solution is to use Zotero for bibliography management and iAnnotate for annotation on iPad (with Dropbox used for transferring PDF files from the desktop computer to iPad).

Zotero is very powerful. When you log on to a webpage of an journal article, the address bar shows an icon which can be clicked to create a new entry in the bibliography AND to associate this entry with the link to a PDF file on the web. Clicking this PDF link allows me to save a PDF copy. Since I don't use Firefox for any other purposes (Google Chrome is much better to surf the net), I can set a Dropbox folder for PDF copies of academic papers as the default download folder.

Then on iPad, launch iAnnotate, click the download button on the top-left corner (which shows the list of folders in my Dropbox), then click the PDF copy folder. This updates the list of PDF files in iPad. You need a WiFi for syncing PDF files between the desktop computer and the iPad, but in my office there is an eduroam wireless network. So there's no problem.

So, after reaching a webpage of an journal article, I only need to click four times (twice on the desktop and twice on iPad). Then I'm able to read a PDF copy on iPad. This is very efficient.

Icelandic volcano ash

Academics in Europe are also victims of Icelandic volcano ash. Our workplace was supposed to be hosting a couple of leading economists from the US from today until early next week, but they canceled the visit to Stockholm. My colleague visiting from Italy told me his home university has had lots of cancellation of seminar talks as speakers cannot fly to Italy. Another colleague is currently stranded in East Asia where he presented his research.

Inviting researchers from universities abroad is an essential part of academic life, to keep up with the latest advances in research. The volcano in Iceland interrupts us from doing this.

One thing that I don't like about Stockholm

Today I'm reminded of one reason for why Stockholm has made my life difficult.

When I work hard, I don't feel like cooking on my own. However, there is essentially no decent, budget quick eatery in Stockholm. All those sushi places are no-nos to me because they are not Japanese sushi but Swedish sushi. (In case you don't know, Stockholm has a sushi restaurant literally at every street corner; and they tend to fall in the budget category for some reason.) Good restaurants are all pricey and not the kind of place to visit alone. Supermarkets do not help because they sell mediocre ready meals. The ICA supermarket's "Bombay curry" ready meal is pretty bad, for example. Swedes do not really understand the concept of curry. It's not just the mixture of colorful spice and creamy sauce.

Eating mediocre foods depresses me, especially when I am tired. As a result, I've started to avoid working hard and to hate Stockholm.

In London, I didn't face this problem because there were some (if not many) decent, budget eateries. I frequented the Brazilian delicatessen next to Tottenham Court Road station (which, sadly, no longer exists due to the expansion of the station) in the evening when I was very busy writing up my job market paper. Supermarkets sold rather delicious Indian curry ready meals. I would buy at least two packs of Indian curry a week and eat them when I had to work till late.

A partial solution to this is to ask my parents and friends in Tokyo to send me packets of Japanese curry ready meal. They are vacuum-packed. But sending a packet from Japan to Sweden is quite expensive. I cannot resort to this option very often.

What should I do? After more than 2 years have passed since I moved here, I still don't know the solution.

Someone who's not really a considerate person would say, "Have a girlfriend who is a good cook or a good companion to fancy restaurants." If things were that easy, I wouldn't complain here.

A thought on democracy

Why does the international community these days criticize a coup while they are quiet about the democratically-elected government's attempt to restrict free media (as happened in Madagascar before the coup) or to extend the term limit for presidency (as happened in Honduras before the coup)?

Without free media, democratic elections cannot replace an bad-behaving government. Without the term limit, the minority who does not support the incumbent may keep suffering forever. (Imagine the US did not have a term limit for presidency, and George W. Bush won the third term.)

The reason is, I believe, the lack of scientific evidence on what aspects of democracy bring about good outcomes. If there's evidence, politicians and people in the media industry are unaware of it. The international community appears to believe that multiparty elections are sufficient. Alternatively, the media does not loudly report such issues as banning radio stations in less developed countries, and so the international community realize something is going wrong in these countries only after a coup takes place.

We should stop this. And I will devote my life as a development economist to tackle this.

Hi from the capital city of Madagascar

On the day of our arrival in Antananarivo, the capital of Madagascar also known as Tana (pictured above), the current and former presidents of the country, visiting Maputo, the capital of Mozambique, agreed to set up a transition government which will supervise presidential and legislative elections during the next 15 months. (See BBC News for more detail.) On the way from the airport to the hotel by taxi, we saw many, many residents of Tana lining up alongside the road, waiting for the current president, whom the international community does not recognize the head of state of Madagascar, to come back to the country.

With my colleagues from Tokyo, I'm visiting Madagascar to launch a research project on the impact of long-lasting insecticide-treated bed nets (famous for its preventive effect against malaria infection) on poverty reduction. If I have time and connection to the Internet, I'll keep updating this blog LIVE FROM MADAGASCAR.

Done with the revision of the last chapter in my PhD thesis

My PhD thesis, completed two years ago, has four chapters. One chapter was already published in a non-peer reviewed journal. Another chapter was published as a book chapter. The third chapter was submitted to and then rejected by a journal and then re-submitted to another journal last April.

Today I finished revising the last chapter (finally) and submitted it to a journal.

Now I can fully move on to new research projects (until journal editors either ask me to revise the submitted papers or tell me that they decide to reject them).

Week of an assistant professor

Push a little bit forward the autocracy network project, joint with a PhD student of my Institute, by reading some published papers on social networks (hence this post) and by listing up the members of the Presidium of the Romanian Communist Party since 1965 until 1974 from Keesing's.

Tabbouli

For dinner with today's seminar speaker, we went to Tabbouli, a great Lebanese restaurant in Stockholm. This is my fourth visit to the restaurant, and the food is always good.

They serve Lebanese wine only (with exception of a couple of South African for some reason). We tried Château Ksara's red wine, and I liked this wine a lot. As I don't have good vocabulary for describing the taste of wine, I just let you read the description of the wine by Ksara itself (a pdf file). I also tried a cup of Lebanese coffee after dinner, which was brilliant with cardamon flavor. (Here's how to brew Lebanese coffee.)

If you don't know what to order because you're not familiar with Lebanese cuisine, just order the set menu at the back of the front page of the menu. That fills your stomach completely.

Day of an Assistant Professor (79)

Finish revising the African democracy paper and submit it to a journal. It took more than 6 months after the first rejection.

Day of an Assistant Professor (78)

Revise the African democracy paper.

Join a birthday party held by a PhD student of my Institute at his apartment in the evening.

Day of an Assistant Professor (77)

Revise the African democracy paper.

Attend a seminar.

Book flight tickets for the business trip to UK next month.

Day of an Assistant Professor (76)

Meet a PhD student to talk about his research ideas.

Resume the long overdue revision of the Africa-democracy paper.

Day of an Assistant Professor (75)

Prepare the presentation later today.

Give a talk on the climate project at my own department's seminar series with my colleague. After that, discuss with my colleagues the comments we received during the talk.

Day of an Assistant Professor (74)

Prepare for tomorrow's presentation on the climate project.

It's Easter Monday, but this kind of thing does not matter to researchers, especially those without a family and/or coming from Asia like myself.

Day of an Assistant Professor (73)

Have a discussion with my colleagues on the presentation of our climate project next Tuesday.

Plan a business trip to UK (Edinburgh, Nottingham, and London) next month.

Day of an Assistant Professor (72)

Learn from the RA that there are some problems regarding the data entry work. Figure out how to solve them and give her new instructions.

Have a chat with a PhD student who took my course last year about his research.

Have a chat with another PhD student about our possible joint research. And read papers relevant for this.

Day of an Assistant Professor (71)

Have a chat with my colleague on our climate project, run some regressions to test some ideas we discuss.

Brush up on my math skills.

Day of an Assistant Professor (70)

Submit the referee report.

Have lunch with my colleagues to talk about our climate project.

Work on the climate project.

A brief chat with a PhD student about our possible joint research.

Ask an RA for data entry, which is necessary for the climate project.

Day of an Assistant Professor (69)

Write a referee report.

Email replies to several people in connection to my work.

Day of an Assistant Professor (68)

Go to Norköpping (pronounced like nor-shopping) by a 1.5-hour train ride for a seminar of the interdisciplinary climate change research project where Japanese urban hydrologists happen to give a talk.

Over lunch after the seminar, talk to a meteorologist on the weather data and to a biologist on the crop yield predication model.

Go back to Stockholm by X2000, Sweden's high-speed train. With my Macbook Air, I try to write a referee report on board. But I have to stop doing it because the X2000 train shakes a lot, making me almost puke.