New born BioPuppy Linux beta version released!

I gladly inform you that, our first version of BioPuppy Linux is out, now. You can download it from http://biopuppy.org

What is BioPuppy Linux

BioPuppy is an electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners. BioPuppy is available as a live CD cum installation CD [and in USB Pen drive] and containing all the required software to boot the computer with ready to use bio-informatics tools. BioPuppy is based of the Puppy Linux. The another objective of this BioPuppy is small in size. Our estimated size of BioPuppy is ~150MB.

More about BioPuppy

BioPuppy contains all the tools available in the basic puppy linux and bioinformatics tools. It provides both standard and cutting edge bioinformatics software tools on a Linux base. It is powerful, configurable and easy to maintain. It has been customized for ease of use and provides an ideal system for scientists handling and analyzing biological data. The Biopuppy is a light weight version of bio OS. Bioinformatics-related customizations include a large number of bioinformatics programs and programming libraries, the addition of graphical menus for much of the bioinformatics software, and links from the desktop to key documentation and applications. The system also includes a comprehensive, categorized and searchable documentation system for bioinformatics software.

Features of BioPuppy

* More user friendly and easy to use for those new to Linux.

* Contains all the necessary Bioinformatics tools. Check the Biology tools already included in BioPuppy.

* BioPuppy will boot from a minimum PC/Laptop with 586Mhz CPU and 32Mb RAM

* Easy to install in Hard disk, USB Pen drive and Compact Flash (CF) cards. No fear on installation for those new to Linux.

* Very small in size (~180MB). But it has everything.

* BioPuppy can run your operating system, programs and store your data on the same CD-RW/Pen drive/Hard disk

* BioPuppy contains extensive help files for ALL its programs and Bioinformatcis tools with screen shot.

* Can easily update new version.

* Bring all your programs, tools, moves, songs with light weight BioPuppy Linux in a single USB Pen drive.

Biology softwares included

Sequence Analysis Tools :: Sim-4, Tigr-Glimmer 2, Genewise, Muscle, Sigma, HMMER, Clustal-W and mafft

Structure Prediction Tools :: mfold, gibbs

Protein Structure Analysis Tools :: Garlic,Rasmol

Phylogenetic Analysis tools :: Fast DNA, Phylip, Phylodraw

Protein Modeling :: Modeller

Docking :: MGL Tools (Autodock tools, Python Molecular Viewer (PMV), Vision)

System Biology :: Copasi

On-line tools :: BLAST,EMBOSS

For more please visit http://biopuppy.org

Your contributions are almost welcome!…

Some screen shots

How developers/companies are earning money from Open Source environment?

Free and Open Source Software (FOSS) need not a free of cost. We can earn money in some ways from Open Source softwares by directly and indirectly.

* Hope you know, we dont have any official supports for Open Source softwares. Take a OS s/w; Sale it with free of cost for your customer. When they want support, you just charge some money.
* One important drawback in OS is, no ready made development environment and taking more time duration for setting up a environment. if you will do every thing in a single package, then you can earn more money from OS. For example, still we dont have any ready made working environment for embedded linux. We have to install more tools and need to configure lot of things. Its an nightmare for developers. If you possible to collect all the tools, configure it and ready for sale, you can earn more money, I m sure.
* You can also earn money by teaching OS tools and softwares, like provide training.
* You can also earn money by providing installation setup/supports for an company/organizations. CDAC is d example in this case. They are doing this business for all the government org from BOSS linux.
* My-sql is an open source DB. Recently, Mr.Brain [Owner of mq-sql]sale his OS project MY-AQL to another company for some millions. But it took around 6 years for earn this money from his open source project.
* Sale a OS operating system CD/DVD is an good business and more…

Why the companies are starting a OS software
====================================
You may ask this question, definitely. Now we can see why a company/developer start an OS project.
* You will get more contributions from community. So that your product will be stable soon.
* Get more contribution from community. You no need to recruit more people for this project.
* Google encourage more OS activities like Google SOC and this is the best example company for earning more money from OS by directly and indirectly.
* Intel have a big OS community. So that they are getting contributions for writing drivers for their processors. They have lots of other OS projects too, http://oss.intel.com/en-us/
* NOKIA, have a OS community. Initially they started with couple of OS projects. Now they have more than 25 projects in a short period. Through this OS activity, they are getting more contributions for their application development and others. visit http://opensource.nokia.com/
* {After NOVELL earned more bad issues from communities, once tied with Microsoft} Now AMD supports OpenSUSE project, http://www.opensuse.org/
* nVidia have a OS community and they are getting more contributions for writing drivers for their devices.
* There are lots of companies are having OS activities. Coz, they are getting credits indirectly, compare with what they are earning money by directly.

* For more details about Open Source business plan refer this link, http://www.opensource.org/advocacy/case_for_business.php

Howto get a embedded system job and what i want to do for that.

I thing recently I am getting more queries related this topic.
I would like to share my suggestions with all the freshers in embedded system. We have already discussed about it. But still the freshers not get any clear idea about, howto get a job in embedded system. Hope this thread ill help them to understand first, what the industries are expecting from them. I request you to post all your comments here, if you have any.

Dont do/think
===========
* Entry for freshers in embedded system is really easy…
* I ill get a job immediately, coz i have a embedded system certification from a great -ABC- institution.
* I have fully fitted for embedded system field. Coz I have completed all the modules include, C,C++,Unix, Device drivers, Micro controllers and RTOS. Oh….I am great. What do you want more….
* If i cant get any job in this field, then i just simply put a 1+ yr fake experience and try for job. The recruiter easily believe me. Then I ill get a job easily. Oh…I am really so brilliant….
* If i add one or two projects [especially some rtos projects like vxworks ]in my resume then i can easily get a job.
* I have 90% marks in all d certificates. The interviewer easily accept me for this embedded system field.
* I have done a embedded system project in a big MNC embedded systems company. So i m eligible for getting a job easily.

Then What I want to do/Think?
========================
* What ever it may be, You should learn from in-depth. For hardware engineers, learn from flipflop, micro processor….etc. For software engineers, learn from compilers, linkers, OS concepts….etc.
* Do some real time projects from what you have learn. For example, u have 6 modules in course, try to do minimum one project for that module by your own and d project should b related with industries use.
* Try to utilize your lab facilities. Especially your lab hardwares. Hack it, what ever you want.
* Learn The Linux OS for embedded system. Coz it has good future in embedded system and in India. Coz Linux is exactly suitable for embedded system field other than windows. Another reason is, you can hack the linux from top to bottom. Coz its open source and no need to depend upon any proprietary softwares. So that you can learn more and get more rel time exp.
* Plan to buy a hardware board like ARM 7 or others. You can get the hardware from 3k to 10k based on configuration. Using this boards, you can feel the real time exp for porting, cross compilation, linux, emb linux, rtlinux and other rtos. If you got these experience, your interviewer will satisfy almost.
* You should sharp your language skills like C,C++,Java….etc. This is very important for s/w embedded system engineers.
* Try to contribute to some international forums, mailing lists and magazines like www.linuxdevices.com, www.embedded.com. So that you can update your knowledge in this field and whats happening in the current embedded field on industries side.
* Try to contribute some embedded system open source projects already available in internet. Go through the site, www.sourceforge.net and search for embedded system project. you ill get thousands of project related embedded system. Definitely, you will get nice experience on this field.

What are the available chance for getting a job in this field
===========================================
(1) Select a embedded system company in your college placements. Avoid d s/w companies like CTS, Infosys…etc, if you have a confident to get a job in embedded field/company.
(2) If you dont have d placements, send your resumes for selected embedded system companies, even you are a fresher. Insist your full of interest in embedded system.
(3) You may join some embedded system courses aft 6 months you got finished your degree. During this 6 months, you can try for freshers job. You may get some placements through your training institute. But this is not guarantee. Its depends the institute and your capability. But d course is not necessary for embedded system, if you have capable of learn by your own and full of self confident. My personal opinion is, I wont suggest you to do a course. Coz in india all d institute are not teaching good in embedded system. All are money minded.
(4) If you have done some good projects followed by the “what to do” steps, you have more chance to get a job in this field.
(5) If your intention is only for getting a job in this field, then dont look big MNC companies & big salary. You have lots of small embedded companies are there. For entry, this is more useful for you to learn a lot in this field other than a big company. so your first preference should be small/startup companies.
(6) Suppose u cant get a job in this field after one year, now u can put 1+ yr fake exp with reasonable projects. I did nt suggest this idea in previous topic. But here I suggest you; Coz some times it will work. But its not guarantee and more risky. At the same time, you should have all capable of doing all the stuffs equivalent to 1+ yr exp person. Interviewer easily identify you; But he may prefer you, due to some reasons. First one is, you have all d stuffs for manage every thing without exp. 2nd one is, they have forced to recruit a person for emergency.
(7) Last but not least, keep on trying ,even u crossed more.

I wish you all the best for your best career in Embedded System….

Solution for "/bin/sh: Can’t access tty; job control turned off" error

Recently, we tried to boot our customized Puppy live linux from pen drive in our Intel 201GLY Mini-ITX board. But we gor the error:: /bin/sh: Can’t access tty; job control turned off
For the last one month we cant solved this problem. Now we solved this problem .
The solution is, just boot the kernel with the option, "acpi=off".
The following steps will provide you more details,

1. Boot your computer so that GRUB is displayed.
2. Press the "e" key to go into edit mode.
3. Press "o" to add a new line to the script.
4. Type the following: acpi=off irqpoll
5. Press the Escape key.

In the event that acpi=off doesn't work try replacing the entry above with one of the following:

• acpi=force irqpoll
• nacpitimer irqpoll

Hope this info helpful for the people those who are seeking the solution for this problem.

Howto create Bootable USB Pendrive for Puppy Linux

How to create an bootable Puppy Linux for USB Pen drive:
--------------------------------------------------------------------------------------------------
I tried this step for my IGB Transcend USB pen drive. Hope it will work in other brands also.
Download puppy-3.00-seamonkey.iso from puppylinux.org
Here the bolded words are commands.
login as a super user in your host linux
Insert your pendrive.

Mount d pen drive:
--------------------------------
#mkdir /mnt/usb
#mount -t vfat /dev/sdb1 /mnt/usb/
If you want any backup of your pendrive, take a copy from it.

Fdisk:
----------
# Now type fdisk -l to list available drives/partitions (note which device is your flash drive Example: /dev/sdb). Replace all instances of x with your flash drive letter. For example, if your flash drive is sdb, replace x with b.
# Type umount /dev/sdx1
# Type fdisk /dev/sdx

* type p to show the existing partition and d to delete it
* type p again to show any remaining partitions (if partitions exist, repeat the previous step)
* type n to make a new partition
* type p for primary partition
o type 1 to make this the first partition
o hit enter to use the default 1st cylinder
o type +750M to set the partition size
o type a to make this partition active
o type 1 to select partition 1
o type t to change the partition filesystem
o type 6 to select the fat16 file system
* type n to make another new partition
* type p for primary partition
o type 2 to make this the second partition
o hit enter to use the default cylinder
o hit enter again to use the default last cylinder
o type w to write the new partition table

# Type umount /dev/sdx1 to unmount the partition
# Type mkfs.vfat -F 16 -n usb /dev/sdx1 to format the first partition

"Alternately you can try mkfs.vfat -F 32 -n usb /dev/sdx1 (doesn't always work)"

# Type umount /dev/sdx2 to ensure the partition is unmounted
# Type mkfs.ext2 -b 4096 -L casper-rw /dev/sdx2 to format the second partition
# Remove and Re-insert your flash drive
# Back at the terminal, type sudo apt-get install syslinux mtools [if you are using debian/ubuntu]
# Or you can install with yum install syslinux mtools [if you are using fedora]
# Type syslinux -sf /dev/sdx1

Copy the iso files in local directory:
------------------------------------------------------------
#mkdir puppy_temp
#mkdir puppy_usb
#mount -o loop puppy-3.00-seamonkey.iso puppy_temp
#cp -a puppy_temp/* puppy_usb
Note:: From this step, we have copied the content of the iso image into a new directory.so you can work on it. If you try to copy this data directly to the USB memory stick, it will not boot because we need to fix the position and the naming of the files. With the consolde opened, enter the following commands.

Boot file modification:
-------------------------------------
#cd puppy_usb/
#mv isolinux.bin syslinux.bin
#mv isolinux.cfg syslinux.cfg
cd ..
Now mount the pendrive again and copy the puppy_usb directory files to your pen drive.
#mount -t vfat /dev/sdx1 /mnt/usb/
#cp -a puppy_usb/* /mnt/usb/
#umount /dev/sdx1

Make it bootable:
------------------------------
#syslinux /dev/sdx
Note:Ensured that you have installed syslinux. If you will get the error "command not find". Then you need to instal syslinux
Now reboot your computer, leaving the pen drive inserted; Modify the BIOS boot device and let the system ot to Puppy on the memory stick.

Hints for BIOS setting:
---------------------------------------
Reboot ur computer and press F2 for enter into BIOS setting. F2 may be varied in your pc. check the pc when it boot.
Once you entered the BIOS setting, come to "Boot sequence" option. Select the USB-HDD or USB-ZIP and move it for boot first. Means, set the highest priority.Now save it and reboot.
Play with Puppy!...

How to configure Your Cell phone in Linux OS for Internet connection

I tried this steps in Ubuntu OS from My Sony Ericsson K510i. I am using Airtel Subscriber.
Hope it will work in other Linux distros also.

Step 1:
=======
Start your pc and now enter id root and password (you must be knowing that!) Now open terminal and type "dmesg" It will detect all the device connected with your pc including your (usb, serial ) data cable.and it will display log in the same terminal read that log carefully now check which port has been detected by it. It detected ttyUSB1 on my pc.

$wvdialconf /etc/wvdial.conf
it will detect ur mobile and it will write the value on wvdial.conf file in etc directory.



Step2
=====
Now open the file /etc/wvdial.conf from your terminal,
$vi /etc/wvdial.conf
In that file, you can show a existing configuration. You just remove all the lines and paste the following code.

#Paste the following lines to your wvdial.conf file
[Dialer Defaults]
Modem = /dev/ttyUSB1 #note1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
stupid mode = 1
Modem Type = Analog Modem
Phone = *99# #Note2
ISDN = 0
Username = a
Password = b
Baud = 115200

#Note1: May be varied depends upon your hardware config.
#Note2: First check your mobile phone dial No.

step 3 Open the file, /etc/resolv.conf and enter following lines. Now dont delete the existing lines. You just append.

service named start
nameserver 202.56.230.5
nameserver 202.56.250.5
nameserver 127.0.0.1

Now log out and log in as User and open terminal now type su - and press enter, than type root password for your super user mode.
Then type wvdial R in your terminal
Hope now you are connected to Internet now enjoy surfing . If u want to disconnect than just press CTRL + C or killall pppd
And it will disconnect active connection!.

Sound card problem in Acer Aspire 4520

Recently I bought a Acer Aspire 4520 laptop. I installed some Linux OS includes Fedora 7, Open SUSE 10.3, Ubuntu Fiesty and debian. But None of my installed OS detected my sound card. Finally I removed all the distros and installed Ubuntu Gutsy 7.10 and then downloaded latest ALSA-Driver from www.alsa-project.org. Installed this driver. Now My sound card is working fine. Here I have noted the steps what I have done for my sound card problem. It will useful for someone to search solution for this problem. And here I have given the link for ubuntu forums. Seems, more people getting this problem. Ref this page, before you start to install the alsa,

Steps for installing the ALSA Driver:
-------------------------------------
* Installed Ubuntu Gutsy version for 64 bit
* login in console mode
* By default, the nvidia driver installed. Install the driver by using
$apt-get install nivida-glx-new
$sudo nvidia-glx-config enable
Then retsart the Laptop. Now almost the video problem will solved.

* Updated the packages.[kernel also updated]
* Installed build-essential from package manager. It has resolved lot of dep problems.
* Downloaded alsa-driver-1.0.15rc3.tar.bz2
* Untar it
* $./configure
* $make
* $make install
*$./snddevices
* sudo vim /etc/modprobe.d/alsa-base
added this "options snd-hda-intel model=acer" in almost last line. Aft that save it.
* Reboot
* Now my lapy logged in with nice Ubuntu sound. The sound card working fine.
Thanks to ALSA and Ubuntu....
This is the common steps for all the distros.
Have the Fun..