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1. How do major differences among lineages evolve
2. What is the relatedness between organisms?
3. What is adaptation like in these organisms?

1. Origin of genetic variation: via mutation and migration
2. Sorting of that variation: variation can be affected by genetic drift and natural selection for instance. For those drawing a blank on genetic drift...it is the change in allele frequency over generations...for those of you drawing a blank on allele...an allele is essentially a gene or better yet a specific version of the gene. So one gene can have more than one flavor. An allele is a particular flavor of that gene as determined by its sequence data.  For those of you drawing a blank on gene...click over to the nyan cat you tube video--be entertained and dont come back to this blog until you know what a gene is.
3. Simultaneous genotyping of neutral and adaptive loci (for population genomics): neutral loci provide a genome wide background that gives you estimates of effective population size and can be used for phylogeography. Adaptive loci are outliers from the neutral background and can lend insight into selective sweeps or local adaptation.

• You can call SNPs simultaneously
• Its cheaper
• Better than a SNP chip because a SNP chip may not be applicable to any other organism other than the one you designed it for.
• You can do this on 1000s of genomes in a matter of weeks
• Reasons not to? If you are trying to analyze a genome that has shorter LD blocks. LD is linkage disequilibrium where you have linked loci. When you are at linkage equilibrium in your genome then essentially there is no linkage in the genomes, everything is random everywhere, shuffling ad hoc. In linkage disequilibrium you have blocks of loci that carry each other forward evolutionarily and are conserved or selected for together.

1. You have sites within a genome that corresponds to sites that can be cut using a restriction enzyme.
2. Once cut you can ligate the amplification primer, sequencing primer and barcode to the sticky overhang left from the cutting.
3. You can finish the other blunt end with an adapter, amplification and sequencing primer to allow for amplification prior to NGS.
4. You then follow the normal protocols for next generation sequencing and get well...a f*!k ton of data to say the least... see figure below...

Lecture Presentation: Bill Cresko, Univ of Oregon

1. Make sure your barcodes are sufficiently different from one another because later on you will be specifying parameters and allowing for mismatches. So if you have two barcodes different by one or two nucleotides and you allow later on for 1-2 mismatches youve effectively made your two distinct barcodes one and same in the eyes of the computer and you will not be able to tell those two samples apart from each other and as Julian stated..."Ive done it, its a mess".
2. Make sure your shearing yields optimal lengths of ~300 bp unless you have a reason not to given your platform or technique. For Illumina, long fragments interfere with sequencing amplification--so just say no to long fragments.
3. Through experiementation the Cresko lab has determined that random shearing improves the distribution of coverage across your genome for your sites versus other methods that dont use a shearing step.
4. Number of sites versus depth versus number of samples. You really ought to have 20-50x coverage ideally. Well if you have a million reads, 100x depth, 1000 samples youve only got an average coverage/sample of 10x...not ideal. So take this into consideration.
5. Distinguishing true SNPs from sequencing error: RADs uses a maximum likelihood method to determine if SNPs are significant to be called. But keep the above in mind too...if youre coverage is still low, your statistical test will no yield significant results for SNPs even though they might be truly there. So keep coverage in mind.
6. The number of barcodes you should use? Well barcodes are typically 5-8 nts long and need to be sufficiently different to be able to sort. So consider that.
7. Dont ever forget library quality!! If your sequences suck your downstream processing and analysis will too!  
6. The number of tags you should use? Depends on your enzyme and genome size. Use this fantastic little formula ala Cresko...

Adapted from Cresko Presentation, Workshop on Genomics 2013

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Birthday Hari ini 13 tahun lagi aku boleh pencen Cikgu!!

Razor-qt is desktop which a KDE-ish

• highly configurable,
• easy-to-use,
• light weight(low hardware requirements),
• fast desktop environment based on Qt.

Razor-qt cosists of various components:-

• Panel -you can add plugins, behave like GNOME 2.X applets
• Desktop with icons support
• Application launcher(razor-runner)
• Settings (Configuration center)
• Sessions

 Razor-qt works with various WMs, but Openbox seems to be the preferred window manager.

Installation:-

 I have openSUSE 12.3/ GNOME 3.6 installed, the following procedure was used to install Razor-qt.

Pre-installation:-

 First i turned-off Autologin , created "new" user and used this new user for logging into Razor-qt. For details see User Management on GNOME 3.X

Installation using YaST

Add repo

Add the following additional repo using YaST:-

http://download.opensuse.org/repositories/X11:/QtDesktop/openSUSE_12.3/

Install Packages

Install the following packages using YaST Installer

• Base packages
• razorqt
• pavucontrol -simple GTK based "mixer" for PulseAudio
• Additional packages
• qtdesktop - Will pull in various "Must have" Qt applications :-
• juffed - Simple tabbed text editor
• nomacs - Lightweight image viewer
• qlipper - Lightweight clipboard history
• qterminal - Advanced terminal emulator
• quiterss - QuiteRSS - RSS/Atom aggregator
• qupzilla - Web browser based on WebKit core
• qxkb - Qt keyboard layout switcher
• qpdfview - Tabbed PDF Viewer
• screengrab - Screen grabber
• clementine - A cross-platform Music Player based on Amarok 1
• smplayer - Complete Frontend for MPlayer
• speedcrunch - A calculator with history display
• vlc - multimedia player for various audio and video formats
• qbittorrent - A Bittorrent Client built with C++ / Qt4

Installation using zypper

Add repo

open comman launcher(Alt+F2) and open terminal using command ("gnome-terminal") and run following command:-

sudo zypper ar -c -f -n QtDesktop_openSUSE_12.3 http://download.opensuse.org/repositories/X11:/QtDesktop/openSUSE_12.3/ QtDesktop_openSUSE_12.3

Install Packages

Run in the following command in terminal to install the desktop

sudo zypper in razorqt pavucontrol qtdesktop

Razor-qt Overview

 At first time login, Razor-qt provides a dialogue box with a list of window managers and I chose Openbox

The default desktop looks conservative with a touch of gloss. The analog clock adds a nice touch to the desktop.

We see a traditional main menu (Alt+F1)

 Lot of plugins / applets can be added to panel by right clicking on it. We can see Application Menu, Quick Launch, Task Manager, Colour Picker, Lock Tool, CPU Usage tool, Network Usage tool, Show Desktop tool etc.. added in the screenshot below

 Each plugin on panel can be customised. Task Manager can be customised to make opened applications look like squares instead of rectangles.

  Desktop icons / items can be added by creating launchers inside ~/Desktop folder by using commands like "gnome-desktop-item-edit 1.desktop"

 

  Razor runner makes launching applications keyboard friendly (Alt+F2).

 

Razor Configuration Center

 The Razor Settings applet / plugin on the panel is very useful in configuring the desktop. "Razor Session Configurator" can be used to make applications like Artha(Dictionary tool) to start along with the desktop.

 To change themes we need to use both "Openbox Configuration Manager" as well as "Razor Appearance Configuration" .

 "Razor Shortcut Configuration" can be used to create keyboard shortcuts to launch applications easily using keyboard.

Qt Applications

 SpeedCrunch is a cool calculator which has lot of inbuilt formulae

 qBittorrent makes a powerful torrent downloader. qpdfview is a cool lightweight pdf viewer with "tabs" support.

 JuffEd is a good text editor and NoMacs does a good job as image viewer

 QupZilla makes a wonderful webkit based browser and has variety of features like AdBlock, RSS reader, Cookie Manager and web inspector. It also has a good collection of inbuilt themes.

 SMPlayer and VLC (Audio & Video players) play almost anything you throw at them.

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Best Free Android Games

Android has come a long way since its birth. We now have Android 4.2 Jelly Bean for a buttery smooth user experience, Photosphere feature, and whatnot, which is its latest iteration. Its application store, known as the Google Play Store, is now almost as big and as extensive as the Apple App Store in its repository of apps with almost 700,000 applications. And yes, many are free albeit ads-sponsored.

A lot of applications have also been carried over by major app developers from iOS to Android, which makes the latter almost at par with the former in terms of quality applications to offer. Do note that not every application available in the Play Store is compatible to every Android smartphone. Certain apps have specific requirements such as a certain screen resolution, RAM, internal storage, graphics chip, and CPU clock-speed. Well, enough about this and lets start with my review.

Let me enumerate my favorite FREE ANDROID GAMES at the moment. This is Part 1.

1. Jewels - Jewels is a simple, yet quite polished and fun match-3 puzzle game. For me, its a classic! Perfect for killing time!

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2. Gold Miner Classic - Gold Miner is one of most popular online games. Youre collecting the gold nuggets by pressing the screen, the same way you activate the sticks of dynamite which you can use when something else than gold will get in your hands. Between levels you can buy them in the convenience shop. Great and interesting game, you will not gaze away from it! This game is very much like the Flash-based Internet PC game and its so fun!

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3. Glow Hockey - Glow Hockey delivers a new style of hockey game. Easy to play, hard to master. Glow Hockey delivers a new style of hockey game. Easy to play, hard to master. Challenge yourself with the computer opponents! By the way, youll surely love the glowing effects.

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4. Falling Fred - Lead Fred in his futile exercise to avoid the inevitable - becoming a human slice of minced meat. Dodge obstacles, avoid limb damage when possible but remember to keep your head attached to your shoulders or it�s the end of the trip for you. Still, its not all doom and gloom! Regardless of massive injuries, Fred still survives to tell the tale and re-enact his deeds. This is like Temple Run, but instead of running, you are falling...endlessly.

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5. Angry Birds Space  - The #1 mobile game of all time blasts off into space! After a giant claw kidnaps their eggs, the Angry Birds chase it into a wormhole and find themselves floating in a strange new galaxy � surrounded by space pigs! Luckily the Angry Birds have super powers of their own...
Angry Birds Space features 140 interstellar levels on planets and in zero gravity, resulting in spectacular gameplay ranging from slow-motion puzzles to light speed destruction. If you enjoyed playing the other Angry Birds games and, at one point, got bored then this is the game for you.

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6. Eternity Warriors 2 - The battle for Northern Udar rages on! Its been 100 years since the First Demon War tore the land apart. Thanks to the Eternity Warriors the demon threat was held at bay. However the demons have been consolidating their power in a series of Demon Towers built in locations throughout Northern Udar. Youve been tasked with cleansing these Demon Towers and defeating an even deadlier demon army than before... If you like games like DOTA or Diablo, youll surely enjoy playing this one.

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7. Mutant Roadkill - Race through an apocalyptic wasteland overrun with mutants and other hazards. Blast your way through city ruins as you try to escape a world overrun with danger. Drive as far as you can and compete against the world! Can you make it out alive? This is similar to iOSs Zombie Highway game.

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8. Samurai vs Zombies Defense - Play as a Samurai and defend your village against hordes of attacking zombies! Recruit allies and build defenses to stop them! This is very much like Army of Darkness but its free to play! Its the perfect game to play when killing time.

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9. Temple Run - Run for your life! The addictive mega-hit Temple Run is now on Android. Youve stolen the cursed idol from the temple, and now you have to run for your life to escape the Evil Demon Monkeys nipping at your heels. Test your reflexes as you race down ancient temple walls and along sheer cliffs. Swipe to turn, jump and slide to avoid obstacles, collect coins and buy power ups, unlock new characters, and see how far you can run!

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10. Fruit Ninja - Fruit Ninja is a juicy action game with squishy, splatty and satisfying fruit carnage! Become the ultimate bringer of sweet, tasty destruction with every slash. Swipe up across the screen to deliciously slash fruit like a true ninja warrior. Fruit Ninja features three packed gameplay modes - Classic, Zen and the new Arcade, featuring powerups including Freeze, Frenzy and Double Score!

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So there you have it! This is Part 1 of my 10 Favorites Games on the Android platform, which can be downloaded from the Google Play Store for FREE. I hope you like them all.

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Basics concept of Inductors Coils

1 - Inductors

1.1 - Structure of the coil.

Inductor winding several turns back into the ring, painted EMAY Elementary winding insulation, core coils can be air, or a conductive material such as ferrite or steel core from engineering.

Air-core coils Ferrite core coils

Coil symbol on the diagram: L1 is the air-core coil, ferrite-core coils L2, L3 is adjusted core coil, coil L4 as core technical steel

1.2 - The characteristic quantities of the coil.

a) inductance coefficient (Faradays Law)
Inductance coefficient is a measure specific to the induced electromotive force of the coil when an electric current runs through the variable.

L = ⁽² .S.10 ?r.4.3,14.n ^-7) / l

• 
  
  L: is the inductance of the coil, the unit is Henry (H)


• 
  
  n: number of winding coils.


• 
  
  l: length of the coil is measured in meters (m)


• 
  
  S: is the cross section of the core, in m ²


• 
  
  ?r: permeability coefficient of the core material.

b) Comments Resistance
Inductance of the coil is a characteristic quantity for the resistance of the coil current to alternating current.

Z L = 2.3,14.fL

• 
  
  Where: Z L is the inductance, the unit is ?


• 
  
  f: is the frequency unit is Hz


• 
  
  L is inductance, unit is Henry

Taste test of rolling resistance
wire with AC

* Testing of illustration:
Serial coils with bulbs are then connected to the 12V power source
but with different frequencies through the switches K1, K2, K3, while K1
play a direct current passes through the coil strongest (Because Z L = 0) => so the brightest bulb, while K2 closed 50Hz AC coil passing more yey (by Z L increase) => weak light bulb, when K3 is closed, AC 200Hz go winding through the weakest (from highest Z L) => weakest light bulb.

=> Conclusion: Thank resistance of the coil is proportional to the inductance of the coil and is proportional to the frequency of alternating current, alternating current means with higher frequency coil crossing more difficult, DC frequency f = 0 Hz so with DC coil inductance L Z = 0

c) The resistance of the coil net.

Net coil resistance of the resistor, which can be measured by copper
multimeter, conventional coil resistance qualities, the net
relatively small compared to inductance, resistor of resistor called
resistive losses because the heat generated when the coil operation.

1.3 - Nature of charging or discharging of the coil
* Coil energized: When a current flows through the coil, the coil load a form of magnetic energy is calculated by the formula

W = LI ^2/2

• 
  
  W: energy (June)


• 
  
  L: inductance coefficient (H)


• 
  
  I currents.

Experiments on the charging and discharging of the coil.

In the experiment: When K1 is closed, the current through the coil in ascending (generated by the coil inductance against sudden surge currents) so light bulb slowly, when K1 and K2 interrupt both closed, energy loaded in coil form induced voltage darted back through the bulb as light bulbs flashed
=> Phenomena that coil discharge.

2 - Speaker and Microphone

2.1 - Speaker (Speaker)

Speaker is an application of the coil and magnetic field.

4 ? speakers - 20W (Speaker)

Design and operation of the speaker (Speaker)

Composition of speakers:

Speakers include a cylindrical magnet interlocking poles, N pole in the middle
and S poles around, between two poles forming a slit from the magnetic field
hard, a coil is attached to diaphragm and is placed in the slot from,
Nearby diaphragm is supported by a soft rubber diaphragm can help to ease
fluctuating exit.

Activities:
When our audio-frequency electric current (AC from 20 Hz => 20,000)
flowing through the coil, the coil creates magnetic field and magnetic equipment
Permanent magnet pushed out, pushed to make coils oscillating =>
speaker membranes vibrating in and vocalize.

Note: Excellent
for we must not put DC on speaker, because the current one
dimensional magnetic field generated only fixed and deflection coil of the speaker only on a
direction and stopped, then direct current through the coil rose sharply (by
no induced voltage in the opposite direction) so that the coil will be
fire.

2.2 - Micro

Micro

Micro structure is essentially a miniature loudspeaker, the structure Micro Micro has the same speaker but within the larger coil wrapped around a lot so the speaker impedance of the coil is very large microphone about 600? (impedance speakers from 4? - 16?) in addition to the microphone membrane is formed very thin and easy to oscillate when sound effects on.
Speakers are devices to convert electrical current into the microphone, the sound also reverse
again, change audio Micro audio-frequency electric current.

2.3 - Relays (Relay)

Relays

The relay is also a coil applications in the production of electronic equipment, the principle of operation of the relay is transformed into magnetic currents through wires Quon, from schools to form the mechanical force via gravity to perform a mechanical movement as the switch opens, opens the itinerary of an automation equipment etc ...

Structure and principle of operation of the relay

3 - Transformer

3.1 - Structure of the transformer.

Transformer is a device to convert AC voltage, composition includes a primary coil (put voltage on) and one or more secondary coils (voltage taken out of use) and wound on a magnetic core can is laminated or ferrite core.

Symbol of transformers

3.2 - Percentage of ring / vol of the transformer.

• 
  
  N 1 and n 2 call is the number of turns on the primary and secondary Quon.


• 
  
  U1 and I1 the voltage and electric current in the primary winding


• 
  
  U2 and I2 is the voltage and electric current from the secondary coil.

We have the following relation:

U1 / U2 = n 1 / n 2 voltage in the primary coil and two secondary proportional to the number of windings round.

U1 / U2 = I2 / I1
Electric current in the coil on both ends inversely proportional to the voltage, ie
if we take the higher voltage for as small lines.

3. 3 - The capacity of the transformer.

The capacity of the transformer depends section of
magnetic core, and depends on the frequency of the alternating current, active transformer
active in the higher frequency for greater capacity.

3.4 - Classification transformer.

* Transformer and Transformer audio source:

Power transformers toroidal power transformers

Frequent power transformer in Cassete, amply .., transformers operate at 50Hz grid frequency, transformer core using E-shaped leaves and I Tonsilic reassembly, transformer ratios ring / vol large .

Audio-frequency transformer used for reverse-phase transformers and transformer circuits to amplify the speaker in the audio output, also used transformer core sheets made from such Tonsilic source transformer, but leaves tonsilic in audio transformer thin more to avoid losses, audio transformers operate at higher frequencies, so have some lower vol ring, when audio-frequency transformer design it is often worth taking the average frequency of about 1kHz - to 3KHz.

* Transformer & High Voltage pulses.

High voltage pulse transformer

Transformer pulse transformer is operating at high frequencies around tens of KHz as transformer of the pulse source, high-voltage transformer. pulse transformer cores made of ferrite, by operating at high frequency pulse transformer for very strong capacity, compared with conventional power transformer with the same weight, the pulse transformer can give a capacity of tens of times more powerful .