C Quick Guide Learn C programming in simple and easy steps starting from basic to advanced concepts with examples including C Overview, language basics, Environment. C Program to print numbers from 1 to N without using semicolon How to find sum of two numbers without using any operator How will you show memory representation of. R Syntax A gentle introduction to R expressions, variables, and functions Vectors Grouping values into vectors, then doing arithmetic and graphs with them. Step. 05 Bare Metal Programming in C Pt. Valvers. Finally, we get on to a tutorial that moves us away from blinking an LED as we explore the. Video. Core IV GPUReference Material. We need some reading material for this tutorial this is how I put the tutorial together, byreading and studying the manuals available for the Videcore, but for this tutorial mainly theinformation from the Cambridge Raspberry Pi Tutorials. Yes theres a lot of text and more than onemanual but thats the only way you learn Some material thats useful Generally for late night reading This information is less important for now, but worth noting The GPU Videocore IVThe GPU and ARM devices can communicate with each other through a mailbox system. However, dontforget that the ARM and GPU also share the memory space, and so although we have to communicatethrough the mailbox, this is what negotiates settings and a framebuffer. The framebuffer address inmemory is then returned from the GPU and we can go ahead and write to the framebuffer to seegraphics. A framebuffer is a term that really refers to a block of video memory. This video memory is used todisplay pixels on the screen. So we have access to each pixel on the screen and can change itscolour properties. The framebuffer should be at least as big as the screen resolution. The size ofthe framebuffer memory block is given by framebufferbytes pixelsx pixelsy bytesperpixel. NOTE In this tutorial well be using a framebuffer and so wont have any higher levelfunctions like Open. GL or accelerated graphics. Were going to create a simple software renderer. The number of bytes per pixel sets the number of colours available. The Raspberry Pi GPU supports. A palette mode can be really useful as its fast minimal amount of memory requiredfor the graphics and can be really useful for some special effects by simply altering the palette. Red, Green and Blue levelsof the colour of the pixel, and 3. The GPU is generally quite a closely guarded secret. Summary Read the vocabulary. The particular solutions shown here are merely examples. What matters is the underlying purpose enabling the learner to read the program. The main purpose of this page is for people who already know the some assembly and C to see why it is often very beneficial to use a direct assembly. Learn Haskell Fast and Hard Blow your mind with Haskell. The Grymoires Cshell CSH Tutorial. Check out my other tutorials on the Unix Page, and my. Check my blog Table of Contents. C Program For Arithmetic Coding Tutorial For BeginnersC Program For Arithmetic Coding Tutorial GtaIts a specialised processor, but also apowerful processor and most people would like to run code on it, just like were running code onthe GPU itself, but alas the GPU information is still under NDA Non Disclosure Agreement terms. Broadcom however, did release some information and some of the most interesting information is inthe http www. BrcmAndroidICSGraphicsStack. BCM2. 15. 53 Graphics Driver. Ill reference what material Ive got from there as we go. Unfortunately there is no definitive source of information for the Raspberry Pi GPU, only bits andpieces scattered around the web. The GPU is a Videocore IV. As were going to use the mailboxcommunication with the GPU anyway, we can skip a lot of the GPU detail and just concentrate oncommunicating with the GPU to get a framebuffer to use. The mailbox interface is our main entry point into the world of graphics. The interface wasdeveloped and created by a few guys at broadcom. The mailbox interface is software running on the. GPU which receives messages from software running on the arm and returns responses to each messageafter performing a task. Its implemented in the start. SD Card toboot the Raspberry Pi. You can see their discussion about implementing the mailbox on. Github. The mailboxes are defined on Github. The interface were interested in is the. Framebuffer mailbox. This mailbox is responsible for negotiating the framebuffer. We need some code to be able to readand write data from the mailbox and we also need to define the data structure defined by theframebuffer mailbox documentation. The ARM0. 14 tutorial introduces a few new peices of the puzzle. Firstly, as an aid to debugging now the code is getting more complex it introduces the mini UART which means we can have a basic console. As weve bothered with the standard c library we can see how to tie the standard library functions like printf to the UART. Secondly, it introduces the mailbox property interface which is a method of the ARM processor talking to the GPU. If were going to get to the point of generating graphics, we must talk to the GPU This code does generate an animated display, but as well see it is extremely slow to use un optimised software rendering on an RPIIf you want, go ahead and compile it now and plug the raspberry pi into a monitor or television with a HDMI interface. It should work As were now including new hardware into the mix its possible that your monitor or TV doesnt support the resolution and colour depth that the example is hard coded to use. Its an example thats designed to be simple rather than supporting every HDMI panel out there. Hopefully youll have luck with it. Im using an old Hanns G HUD1. DVI HDMI adaptor. If it works, youll see an ever changing display which moves through the colour spectrum, continuously writing to every pixel in the framebuffer You can see the rather boring output on TODOYou. Tube. This tutorial shows how a 7. MHz or 9. 00. MHz processor doesnt give you carte blanche to program in C and end up with an optimised output. In this example there is no vertical sync used, we simply dedicate 1. ARM processor time to drawing the rectangle in video memory and then moving it one pixel before drawing it to the video memory again. In this way we can see the raw speed of the processor at work. Its pretty slow isnt it Well optimise in the ARM0. Getting a UART Text Console. Read that title carefully, not getting a graphics Text Console but insteadgetting some text out of the code to help us debug. As the code becomes morecomplex we need better ways of debugging. A later tutorial will talk aboutusing JTAG but for now we can have the basic UART based text debugging thatgets us out of most holes This requires some hardware. Namely a TTL 2. 32. R 3. V3or equivalent is required. The mini uart described in the AUX peripheral belowis available on the RPI IO expansion headers on pins 8 GPIO1. TXD and 1. 0GPIO1. RXDConnecting the UART to a PC is pretty easy, a quick connection guide isavailable Also, a quick photo of one connected up AUX peripheral. The AUX peripheral includes a couple of communication interfaces which we can put to use. In this tutorial we will enable the mini UART which has RxTx signals available on the IO header of the raspberry pi. We will connect that to an FTDI 3. V USB UART converter and then we can connect Pu. TTY to the COM port and see output from the code We will do some more work on the c stubs to provide uart support in the write system call which is what the likes of printf, etc. AUXBASE. auxtRPIGet. Aux void. return auxillary. Define the system clock frequency in MHz for the baud rate calculation. This is clearly defined on the BCM2. BCM2. 83. 5datasheeterrata. SYSFREQ 2. 50. 00. RPIAux. Mini. Uart. Init int baud, int bits. As this is a mini uart the configuration is complete Now just. Note from the documentation in section 2. ARM peripherals manual. If the enable bits are clear you will have no access to a. You can not even read or write the registers. ENABLES AUXENAMINIUART. Disable interrupts for now. IRQ AUXIRQMU. MUIER 0. Disable flow control,enable transmitter and receiver MUCNTL 0. Decide between seven or eight bit mode. MULCR AUXMULCR8. BITMODE. MULCR 0. MUMCR 0. Disable all interrupts from MU and clear the fifos. MUIER 0. auxillary MUIIR 0x. Biopython Tutorial and Cookbook. Biopython Tutorial and Cookbook. Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck,Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy X1. Last Update X2. July 2. Biopython 1. Contents. Chapter XA0 1 XA0 XA0 Introduction. Chapter XA0 2 XA0 XA0 Quick Start X2. What can you do with Biopython Chapter XA0 3 XA0 XA0 Sequence objects. Chapter XA0 4 XA0 XA0 Sequence annotation objects. Chapter XA0 5 XA0 XA0 Sequence InputOutput. Chapter XA0 6 XA0 XA0 Multiple Sequence Alignment objects. Chapter XA0 7 XA0 XA0 BLASTChapter XA0 8 XA0 XA0 BLAST and other sequence search tools experimental codeChapter XA0 9 XA0 XA0 Accessing NCBI X2. Entrez databases. Chapter XA0 1. XA0 XA0 Swiss Prot and Ex. PASy. Chapter XA0 1. XA0 XA0 Going 3. D The PDB module. Chapter XA0 1. XA0 XA0 Bio. Pop. Gen Population genetics. Chapter XA0 1. XA0 XA0 Phylogenetics with Bio. Phylo. Chapter XA0 1. XA0 XA0 Sequence motif analysis using Bio. Chapter XA0 1. XA0 XA0 Cluster analysis. Chapter XA0 1. XA0 XA0 Supervised learning methods. Chapter XA0 1. XA0 XA0 Graphics including Genome. Diagram. Chapter XA0 1. XA0 XA0 KEGGChapter XA0 1. XA0 XA0 Bio. Chapter XA0 2. XA0 XA0 Cookbook X2. Cool things to do with it. Chapter XA0 2. XA0 XA0 The Biopython testing framework. Chapter XA0 2. XA0 XA0 Advanced. Chapter XA0 2. XA0 XA0 Where to go from here X2. Biopython. Chapter XA0 2. XA0 XA0 Appendix Useful stuff about Python XA0 XA0 Introduction XA0 XA0 What is BiopythonThe Biopython Project is an international association of developers of freely available Python http www. Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C or FORTRAN. The Biopython web site http www. Python based software for bioinformatics use and research. Basically. the goal of Biopython is to make it as easy as possible to use Python. Biopython features include parsers for various Bioinformatics. BLAST, Clustalw, FASTA, Genbank., access to online. NCBI, Expasy., interfaces to common and not so common. Clustalw, DSSP, MSMS., a standard sequence class, various. KD tree data structure etc. Basically, we just like to program in Python and want to make it as easy as possible to use Python for bioinformatics by creating high quality, reusable modules and scripts. XA0 XA0 What can I find in the Biopython package. The main Biopython releases have lots of functionality, including. The ability to parse bioinformatics files into Python utilizable data structures, including support for the following formats. Blast output X2. WWW Blast. Pub. Med and Medline. Ex. PASy files, like Enzyme and Prosite. SCOP, including X2. X2. 01. 9 and X2. X2. 01. 9 files. Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface. Code to deal with popular on line bioinformatics destinations such as. NCBI X2. 01. Blast, Entrez and Pub. Med services. Ex. PASy X2. 01. Swiss Prot and Prosite entries, as well as Prosite searches. Interfaces to common bioinformatics programs such as. Standalone Blast from NCBI. Clustalw alignment program. EMBOSS command line tools. A standard sequence class that deals with sequences, ids on sequences, and sequence features. Tools for performing common operations on sequences, such as translation, transcription and weight calculations. Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines. Code for dealing with alignments, including a standard way to create and deal with substitution matrices. Code making it easy to split up parallelizable tasks into separate processes. GUI based programs to do basic sequence manipulations, translations, BLASTing, etc. Extensive documentation and help with using the modules, including this file, on line wiki documentation, the web site, and the mailing list. Integration with Bio. SQL, a sequence database schema also supported by the Bio. Perl and Bio. Java projects. We hope this gives you plenty of reasons to download and start using Biopython XA0 XA0 Installing Biopython. All of the installation information for Biopython was separated from. The short version is go to our downloads page http biopython. Download. download and install the listed dependencies, then download and install Biopython. Biopython runs on many platforms Windows, Mac, and on the various flavors of Linux and Unix. For Windows we provide pre compiled click and run installers, while for Unix and other. README file. This is usually as simple as the standard commands python setup. You can in fact skip the build and test, and go straight to the install X2. The longer version of our installation instructions covers. Python, Biopython dependencies and Biopython itself. It is available in PDF. DISTdocsinstallInstallation. HTML formats. http biopython. DISTdocsinstallInstallation. XA0 XA0 Frequently Asked Questions FAQHow do I cite Biopython in a scientific publication Please cite our application note 1, Cock et al., 2. Biopython reference. In addition, please cite any publications from the following list if appropriate, in particular as a reference for specific modules within Biopython more information can be found on our website. For the official project announcement 1. Chapman and Chang, 2. Check Wwn Number In Windows 2012. For Bio. PDB 1. Hamelryck and Manderick, 2. For Bio. Cluster 1. De Hoon et al., 2. For Bio. Graphics. Genome. Diagram 2, Pritchard et al., 2. For Bio. Phylo and Bio. Phylo. PAML 9, Talevich et al., 2. For the FASTQ file format as supported in Biopython, Bio. Perl, Bio. Ruby, Bio. Java, and EMBOSS 7, Cock et al., 2. How should I capitalize X2. C Biopython X2. D Is X2. C Bio. Python X2. D OK The correct capitalization is X2. C Biopython X2. D, not X2. C Bio. Python X2. D even though. that would have matched Bio. Perl, Bio. Java and Bio. Ruby. How is the Biopython software licensed Biopython is distributed under the Biopython License Agreement. However, since the release of Biopython 1. Biopython License Agreement. BSD 3 Clause License. This is with the intention of later. Biopython under this dual licensing approach. What is the Biopython logo and how is it licensed As of July 2. Biopython 1. 7. 0 release, the Biopython logo is a. X2. 01. C biopython X2. D. in lower case. It was designed by Patrick Kunzmann and this logo is dual. Biopython License Agreement or. BSD 3 Clause License. Prior to this, the Biopython logo was two yellow snakes forming a double. X2. 01. C BIOPYTHON X2. D, designed by Henrik Vestergaard and. Thomas Hamelryck in 2. Do you have a change log listing what X2. See the file NEWS. NEWS, or read the. NEWS file on Git.