Why linux is liberating …
Tux
There was a time not very long ago when, the first thing I did after buying a computer was to stuff the latest Windows on it. But now, and for some time before now – I have been totally enthralled by linux. It was never a sudden fascination. No one can be fascinated by the command line ! It grew on me till I could appreciate what the linux movement really implied. Therefore, as a little advice and as an exercise in reminiscence – I will reiterate why linux changed me in more than ways than one.
At heart we are all creative. Yes ! You , your aunt , your mom, dad , sister, friend, girlfriend – everyone is built to be creative. Our language skills develop because we continuously improvise with it. Our physical self develops because we push ourselves in various ways to do many different things. We are alive and in the position to rule this planet because of one very important reason – we were creative enough to understand, adapt and then control the multitude of situations that time has thrown at us. For our long term survival, it is this trait that will be our guiding light.
Linux gives you the freedom to be unique ! It liberates you from the necessity to pay for running code on your hardware to create your unique ideas. Because this freedom comes right from the level of the operating system in your computer – it permeates all that you load and run on it (well almost !). Linux is not a product or a device or an algorithm. It is a confluence of ideas of many unique individuals, ideas built to empower the new computer user to create more unique ideas.
But not everyone wants you to be unique and creative. For the business of selling software, you are a better customer if your needs are predictable and your usage of your hardware is in the “standard” range of customer behavior. So it makes great sense for a software selling company to drive consumer behavior to an average line on their demographic map. The line that leads to the pile of money ! And so you are “encouraged” to buy the “propriety” software so that you can be the “power user”. If only you knew what that really means, you would think twice about being a “power user” !
Propriety and paid for software encourages talents no doubt. The money they can generate can fuel the aspirations of vast numbers of capable humans. There are many brilliant people in Adobe making the “best” photo-editing software. There are many talented folk at Microsoft making the next Windows ! But they are all driven to the same goals, their unique ideas snubbed by the same market forces that are providing their living. Amazingly this money flow generates conformist behavior at both ends !
Linux made me realize the joy of being in a position to exercise the full worth my ideas. From a harmless user who could make photos look cool on a screen, I can now write and deliver code that will do any number manipulations real time on any number of photos and serve them from an Internet domain name ! From a lame one trick pony listening to mp3′s and playing games, I have been transformed to a game maker – creating unique playing fields with sights and sounds which draw interested stares from other human beings ! I have been given the freedom to be unique.
There was a time when linux was that thing you put on your computer and typed endlessly on a black screen with white and yellow characters. Linux used to be for the nerds ! Mainly because it was made by some rebellious nerds. The average Joe cannot be expected to make an operating system can he ? But he can be expected to be unique and creative. And that was what made the average Joe the usability expert in the linux community ! To direct the tide toward a more user friendly and beautiful interface. There was KDE, Gnome, Enlightenment, OpenBox, ICEwm and many more gui interfaces for your favorite desktop. These were the reflections of many unique individuals and groups who strove to make the most “suitable” window manager for your system. Some were nerds, some graphic artists, some usability experts and some plain old grannies and granpas who used it and gave the most valuable thing – feedback. They cared to give feedback because they felt empowered by the system !
Today linux is a powerhouse of variety, usability, security and stability. There is a version for everyone. For those who have 20:20 vision to those who can barely see at all ! For those who want to play 3d games on their home PC to those who want to simulate hundreds of molecules interacting in 3d in virtual reality ! For those who want to write remote procedure calls on far away servers to those who just want to use Internet telephony to talk to their children studying in distant countries ! Linux has put many a helpless man back in the driving seat of his survival story.
If evolution can teach us one important lesson it is this – those who can adapt will survive. Linux enables us to be adaptive – to be what the situation demands and not what the software seller wants you to be. To be your own unique self – so that you can add to the creative pool of human endeavor. Linux is what will redeem us in the end from the monotonous zombie like existence that all of us fall prey to. Linux will liberate you not because linux wants to, but because you will never feel comfortable in those software chains again !
The Top Three Absolutely Essential Plugins For Firefox
Over many years of using various browsers to surf the internet – I have realized that there are certain essential things that make my browsing experience pleasant and productive. Various plugins built in Firefox help achieve this functionality. Here is an outline of the first plugins you should be installing on a fresh Firefox install. Please remember that this is from a active browsing perspective – and not about how to prevent certain things from happening.(For example – having a plugin to block ads etc)
Gmarks firefox plugin
The first important ingredient of a good browsing session is continuity! Yes – you have to have some continuity with your previous experiences. Otherwise each browsing session becomes independent of each other and hence non-productive compared to what you could have achieved if you remembered what you were looking at last! But that is what bookmarks are for, right? Yes of course – you have the bookmarks, but what if you are using two computers? Or even worse – you have arrived at a university and sitting at your new computer you wonder how to lug your bookmarks into this machine! The plugin to do all this and more is Gmarks. It helps you use the Google bookmarking service to have a central online repository of all your bookmarks! The Gmarks plugin taps into this resource and presents an alternative bookmarking menu at top in Firefox. The advantage of using Gmarks is that all you have to do on a new computer is load Gmarks and login to your Google account. That is it! All your bookmarks are back! Better than syncing or trying other kinds of roundabout means to get your bookmarks back. Also each new bookmark that you add under Gmarks will be stored forever online! No chance of losing them again!
Tree-Style Tabs Firefox Plugin
The second most important ingredient of a good browsing experience is – organisation. If your tabs are all over the place you will be spending more time hovering your mouse at the top, trying to figure out your own trains of thought! Not only will you be confused, but you will also be unable to do multi-tasking. To your rescue is TreeStyle Tabs plugin for Firefox. This plugin does two simple things – takes your tabs to the left of your main browsing section (especially handy in widescreen monitors) and organizes them in the hierarchy that they were opened. This means that if you click on “open in a new tab” after right-clicking on a link, the new tab appears indented further than the parent tab and directly under it. This sets up a system more like your files and directories. You know which tab opened up which new tab. Also if you are doing two or three tasks in parallel, this makes it possible to visually isolate the different tasks.
Session Manager Firefox Extension
The third most important aspect of a good browsing experience is sessions. You arrive at a point where all the information is in front of you. And yet you do not have enough time to go through all of it just then. Instead of going on a bookmarking marathon – save the session – use the Session Manager plugin for Firefox. Session Manager stores all the tabs open – in a file, called a session file. Later you can reload the session file to get back all your tabs. In an instant you can have all the information that you researched yesterday!
This session functionality can be extended in conjunction with the Gmarks plugin and some free hosting. For example I store my saved sessions in a free online storage account (ex. Idrive, Mozy etc) and bookmark the link in my Gmarks. So all I have to do is load the two plugins – go to the sessions download page from Gmarks and get back all my sessions anytime – anywhere!
So there you have it – the three most important plugins to augment your browsing experience. The Chrome Browser (from Google) which has just entered the market has managed to get sessions and Gmarks – thanks to plugins developed by enthusiasts. It is yet to get the tree style functionality for its tabs. Till that happens Firefox is still on top! Opera loses out in not having a Gmark setup as yet. In a later article we will explore the usefulness of the next five most important plugins.
Maxtox – predicting toxicity online ! Part 1
The famous skull and bones ...
What is toxicity ? This question has been asked by a newbie to biology, as well as the forty year old drug research scientist. The newbie wants to know the meaning of this word, while the scientist wants to know why is it being used to shelve the drug that he had researched for the last decade ! Indeed this word brings doom to a new drug, it can wipe out companies and research worth many million dollars can come to naught.
The thrust therefore now (and for a long time now) has been to understand this term in the clearest way possible before beginning the long and winding road to drug discovery. There are tomes of books and research materials trying to help in this direction, but when it comes to the practicalities – toxicity is a really difficult concept to understand and measure. There are a variety of “standard” experiments and there are a multitude of competing definitions. Today, the new drug discoverer could not be in a more turbulent cauldron of information, definitions and experiments. Even the experiments themselves are long drawn out affairs consisting of many steps and a lot of resource investments.
In recent times a part of this problem has been solved by software tools. These run on HPCs (High Performance Clusters) and serve a variety of purposes in the aid of drug discovery. A few purposes that these tools serve are
- Help in understanding the structure and 3d spatial orientation of the new molecule.
- Help in understanding the activity of the molecule towards a target protein etc.
- Determine the toxicity of the molecule by comparing it to various standards and formulas ( and other molecules)
However a couple of limitations of these tools has always been the processor intensive nature of the calculations as well as the cost if installing the software and the hardware required for running these systems. The build up to the actual predictive numbers was a major hurdle for most fledgling drug companies. Enter Opentox.
So what is Opentox ? Briefly its a worldwide project (funded under FP7 of EU Commission) to get predictive technologies onto the web, where they can be easily accessed by scientists and interested individuals. A part of this project which is being implemented by me is called MaxTox. Maxtox is a predictive algorithm which tries to answer the important question – how toxic is this new molecule ?
Before running into what Maxtox does, lets first understand a little more about this word – toxicity. There a few common definitions abounding on the internet. Here are a few important ones :
- TD50 : Chronic dose rate (expressed in milligrams per kilogram of bodyweight per day) which would induce tumors in half of the number of test animals at the end of the standard lifespan for the specie.
- LD50 : The LD50 is the dose that kills half (50%) of the animals tested (LD = “lethal dose”). The animals are usually rats or mice, although rabbits, guinea pigs, hamsters, and so on are sometimes used.
Mouse for testing !
As we can see there a few important things in these definitions. The first one is the dose rate – expressed in milligrams per kilogram of bodyweight per day. The second is the endpoint – the target species or the organ of a target species. For example the liver of a rat. There could be a series of experiments done on the liver of live rats to quantify the toxicity of a chemical.
In the toxicity definition, you should be able to notice another important thing – although only in a implied form. Its the number of animals that have to be put to death to get these values. This however is the bitter truth about drug discovery – you have to test it in a multitude of animals before it is considered safe for humans. However Maxtox can help alleviate this problem to a great extent.
Ok so lets find out more about Maxtox. Here are a few things that would define this algorithm.
- Maxtox predicts the toxicity of a chemical against a particular end point (like rat liver TD50).
- Maxtox requires existing data of toxicity against the predicted endpoint – preferably a large set of molecule already tested.
- Maxtox compares the new molecules structure to the tested molecules to find similarities.
- Maxtox uses these similarities in structure to make a statistical model – which predicts the toxicity.
Heres a link to try out the service : http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/. Right now there is one model in place so you can get a prediction of only one type of toxicity. Later the intended direction is to have a multitude of models.
In later articles we I will discuss advantages of this algorithm and the internal logic.
