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End Software Patents
February 28th, 2008 under Digital Rights, rengolin. [ Comments: none ]

If you, like me but unlike American legislation, think that software patents are just unthinkable, please join forces with End Software Patents. Spread the word, help your friends understand why it’s inconceivable to claim ownership upon ideas and mathematics, not to say both (as software).

Please note that this is not just a campaign or petition, they’re also offering legal help if you’re stuck with a patent claim or if you need better arguments on why software patents are bad to our business.

Thanks Josh for the link!

Bioinformatics and its problems
February 21st, 2008 under Bioinformatics, Biology, Computers, Devel, rengolin. [ Comments: none ]

For the last two months I’ve been writing a text about software quality in bioinformatics and the first part is done: I finally finished the basic concepts and tasks on why and how to perform software quality assurance in bioinformatics.

The big reasons why I focused in bioinformatics are:

  1. I’m working in a bioinformatics institute
  2. Bioinformatics has LOTS of problems

If you liked the first part (link just above) or would like to know more about my solutions and ideas keep reading. Use the root link as your entry point and go reading by chapter.

I couldn’t do the next/previous links as the wiki software doesn’t have this automatically and I didn’t want to hard-code it in the text (it’s a software quality text, isn’t it?).


  • The text was written very fast, you’ll probably find lots of incoherent phrases and grammar errors, ignore them for now as I’m re-reading and re-writing everything.
  • I’ve put more than I think I should and am now filtering what’s worth staying. I might also add a few more new things.
  • Most code samples won’t work, they’re a simplified language for clarification only.

Do let me know if you think you could add something I forgot or disagree on any concept, the text is in a very immature state yet.

RDBMS, to rewrite or not to rewrite… I got confused…
February 19th, 2008 under Algorithms, Computers, Devel, Distributed, rengolin, Software. [ Comments: none ]

Mike Stonebreaker (Ingres/Postgres) seems to be confused as well…

First he said Google’s Map/Reduce was “Missing most of the features that are routinely included in current DBMS”, but earlier he said to ditch RDBMS anyway because “modern use of computers renders many features of mainstream DBMS obsolete”.

So, what’s the catch? Should we still use RDBMS or not? Or should we still develop technologies based on relational databases while Mike develops himself the technology of the new era? Maybe that was the message anyway…

My opinion:

MapReduce is not a step backwards, there are sometimes when indexing is actually slower than brute-force. And I’m not saying that on insert time the indexes have to be updated and so on, I’m saying in the actual search for information, if the index is too complex (or too big) it might take more time to search through the index, compute the location of the data (which might be anywhere in a range of thousands of machines), retrieve the data and later on, sort, or search on the remaining fields.

MapReduce can effectively do everything in one step, while still in the machine and return less values per search (as opposed to primary key searches first) and therefore less data will be sent over the network and less time will be taken.

Of course, MapReduce (as any other brute-force methods) is hungry for resources. You need a very large cluster to make it really effective (1800 machines is enough :)) but that’s a step forward something different from RDBMS. In the distributed world, RDBMS won’t work at all, something have to be done and Google just gave the first step.

Did we wait for warp-speed to land on the moon?! No, we got a flying foil crap and landed on it anyway.

Next steps? Many… we can continue with brute-force and do a MapReduce on the index and use the index to retrieve in an even larger cluster, or use automata to iteratively search and store smaller “views” somewhere else, or do statistical indexes (quantum indexes) and get the best result we can get instead of all results… The possibilities are endless…

Lets wait and see how it goes, but yelling DO IT than later DON’T is just useless…


This is not a rant against Stonebreaker, I share his ideas about the relational model being far too outdated and the need for something new. What I don’t agree, though, is that MapReduce is a step backwards, maybe not even a step forward, probably sideways.

The whole point is that the relational model is the thesis and there are lots of antithesis, we just didn’t come up with the synthesis yet.

Pangea day – girls in Africa need your vote!
February 18th, 2008 under rvincoletto, World. [ Comments: 1 ]

Pangea Day aims to ‘tap into the power of film to strengthen tolerance and compassion while uniting millions of people to build a better future’.

Twenty films will be selected to be shown on 10th May 2008 all around the world. Each film selected will receive $3,000 and the opportunity to pitch to Participant Productions (Jeff Skoll’s company). The winner will receive $20,000 to develop their treatment. This would be great for Camfed! (Yes, where I work ! )

If you haven’t already joined up to www.youtube.com, then please do so and view and vote for our film – ‘Two Friends: The Promise of Africa’s Future’ – which can be found here: ‘Two Friends

The more votes and the more hits, the greater possibility our film will be noticed! And please get your friends to vote too!


Help us, Obi-Wan Kenobi; you’re our only hope…
February 18th, 2008 under Articles, Computers, OSS, rengolin, Web. [ Comments: none ]

After Yahoo! rejecting MS offer and all the fuzz about Yahoo! takeover now Yahoo! itself is breaking apart

No wonder the shareholders are mad, Yahoo! has been falling to pieces since Google got into scene and now with the $31 / share offer when it was barely holding it self above $20 the shareholders saw all the return for their investment happening in a very short time, what might be the last chance they have to see any money back at all.

So here’s a bit of futurology:

David Filo moves to Hawaii, shareholders sue Jerry Yang and he’ll end up very poor on his own Caribbean island, Yahoo! is bought by Microsoft by half the price (after the lawsuits there will be few left) and the shareholders will be very happy to, at least, get some money back.

All FreeBSD / Apache / PHP will be converted to Windows 2003 Server / .NET / C# and Yahoo! services will be even worse than they used to be, Microsoft will take the users and force them to start using Google services (no one likes to eat crap anyway) and Google will be the last hope of the Internet.

Fortunately Google is by far more efficient than Microsoft and Yahoo! together (it’s not that hard anyway) and it’ll be piece of cake to take them both down while still holding their hats with the other hand. I just hope Google doesn’t try to dominate the world as Microsoft is attempting for decades, they probably know by now that it’s like reaching the speed of light, the bigger you are the more energy you need to increase speed.

Microsoft and Yahoo! will still exists for a loooong time and Google will have a bit of competition for a while, at least until the “next-Google(tm)” shows up and put all three in the sack “with a wave of her hand(tm)” and the cycle will start all over again.

Let’s hope for the best, whatever that is…

True wisdom from randomness
February 2nd, 2008 under Algorithms, Fun, rengolin. [ Comments: none ]

You can live a whole life and remain stupid but a stupid program using a pseudo-random number generator and a clever algorithm (Markov’s chain) can excel us quite easily:

  • Input: The GNU GPL license
  • Output:

    “GNU General Public License along with you add to sue for details.”

  • Input: man perl
  • Output:

    “PERL (higher numbers usually being affected by wraparound).”

  • Input: My own wiki
  • Output:

    “Bioinformatics is a physicist (definitions of enforcing standards but it puts wrong things can build complex information systems and nothing is totally unacceptable for every new piece of giving generic answers.”


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