Covering the bioinformatics niche and much more

Milking Research Papers, or Recurrences of the Same Topic

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Milking research papers is not the field of research of milk and derivatives; it’s just the ever increasing number of papers from the same group of authors that are basically the same thing, with different clothes. I’m talking only about Bioinformatics, but I don’t doubt that it can be found anywhere.

It used to be create the software, publish the paper, and if you don’t forget about it, create a new version and publish again. Wash, rinse, repeat. I’m guilty of that, with WinPop, but versions were light-years apart from each other. Now the tendency is to publish the software, publish the method, then the new method, new version(s), web version, portable version. Wash, Rinse, Lathe, Rinse, Wash, Repeat.

I hope we can invent some other media to run scientific software, maybe some day I will be publishing a Google TV version of some alignment software. Maybe.

11:11, November 11th

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In Flanders Fields Lieutenant Colonel John McCrae Canadian Army

In Flanders Fields the poppies blow Between the crosses row on row, That mark our place; and in the sky The larks, still bravely singing, fly Scarce heard amid the guns below.

We are the Dead. Short days ago We lived, felt dawn, saw sunset glow, Loved and were loved, and now we lie In Flanders fields.

Take up our quarrel with the foe: To you from failing hands we throw The torch; be yours to hold it high. If ye break faith with us who die We shall not sleep, though poppies grow In Flanders fields.

A Positive Note

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I have been condemned and lost one reader today (maybe more than one, I know I still have about 4) and I admit I have been extremely negative in my posts. But my own perspective in life is that what I can do with the lemons I get. I promised to write one post per day in 2010, and I’m still very far from reaching this goal, something I will still try to accomplish. I also started blogging in the Python Software Foundation blog, which consumes a bit more of time.

The sad truth is that I have no will to write; rephrasing, I’m not compelled to write. I’ve been away from social websites – that’s a good thing – and I don’t know what is going on in the world. When I say social websites, I don’t include Hacker News, a website I wouldn’t be able to live without. I have been reading a lot, actual books, and working.

On a positive note, I cannot praise Zotero enough. It’s the best reference management system out there, hands down. Kudos to the development team and everyone at Zotero. Keep up the good work!

PLoS Blogs: I’m Excited

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Indeed I’m excited for PLoS blogs: they don’t have a cult leader (yet?!), the lineup is good and well balanced and they posts are good (so far).

I just hope it doesn’t become the first blog community where reading is free but you have to pay to publish your comment. After all they will be spending a lot of money of server time and bandwidth.

Mendeley Open-source: Possible Revenue Streams

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If you’re reading this blog for the first time, you’d think that I’m Mendeley’s #1 fan. If you’re a long time reader (the five or six regulars), you might think I’m going crazy, or Mendeley has bought me (if so I haven’t received the cheque or wire transfer).

But, as I’m giving a whole business model to them, let’s just have it in a complete package. I mentioned why Mendeley open-sourcing its apps would make sense. But still they have people backing them up, otherwise they wouldn’t be able to hire everyone and their cousins. They also need to put food on their families plates, even though the backers might be millionaires.

It really makes sense for Mendeley to open-source and there’s an easy way for them to make money even being completely open. They have something no one has, with the exception maybe of Thomson-Reuters. They have a rich database, they have information, precious data. But stored data doesn’t make a profit. Stored data is there to be analysed, it needs to be crunched, checked, tabulated. Why not charge for it? You’re a journal publisher and want to check how many people are reading what, how’s the competition doing? Yep, you can check our db, and there’s a price to do that. You’re a company that wants to index your publications, metadata, etc? We provide the service and you pay a fee. You’re a grad student that wants to do some research? Hey, you have 100 free searches every day for free, if you pass over that number, you pay a penny for each extra search.

There are many other options of revenue. You can make deals with libraries and offer them database and distribution rights in order to mine their internal searches, etc. Each University will have its own rules, so that might be slow in the beginning, but if someone pays millions to have PeopleSoft installed, they can pay something to have the clever guys from Mendeley to take care of their library back-end (don’t mess with librarians).

I was criticized by Rod Page that by opening Mendeley’s source it would be pointless, but from the perspective of a comapny PR and community support that would be huge. Open what you can, profit from what no one has. Who knows if there’s some brilliant hacker that only with the API can make a better desktop client? Are you afraid of that Mendeley? Or you are afraid that your code is so messy that you are going to be criticized for it?

At this point we can only conjecture on what they are going to do, they want you to open your data, but they don’t want to give you something else back, something that won’t cost them much and at the same time will make them the champions of a community that is known to give things back.

They ask what side are you on, but they don’t tell where they are. At least not completely.

Campaign: We’re Open, Mendeley

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Due to overwhelming support I have received throughout the day on my prediction that Mendeley is going open source, I’m starting the campaign,

We’re open, Mendeley

Let’s show our community power and inundate Twitter, Facebook (I created a group on Facebook), Friendfeed and all social network sites with requests for making Mendeley Open Source!

Why It Makes Sense, Re: Mendeley Open Source

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Of course it makes sense. For better or worse, Mendeley has a tight following in the among the open-sciencers and associated hipsters, that would pay, donate and help keep the company afloat (see Reddit, even though they were bought by the nasty Conde). Also, going open-source would be a gutsy move, a heck of a PR turn around. It would silence its critics (me included) and it will use the momentum to improve their products and the crappy desktop app.

Imagine the scenario where hundreds of clever people will be buried in Mendeley’s code trying to tweak it and make it better, faster and more reliable. These are very clever people and they work usually for nothing, maybe a like on Friendfeed or an invitation to the next Science Online meeting (let’s make it in some resort location). Mendeley will also have the opportunity to show their corporate clients that they have the community behind them and the community will go wherever Mendeley will go. It’s a win-win, there’s nothing to lose. And all I’m reading and feeding from my sources suggest that’s the differential in Mendeley’s history. They have the opportunity to put their app where their mouths are.

What side of History are you on, Mendeley?