Hello All,
I have been using Arduino Due and it has been a very powerful board . I wanted the board to be used as an regular development board without the arduino environment by making use of Kiel MDK .I went through the site and they needed an jtag cable to download the code onto the board , is there a way to download the code to the board over the regular USB connection.
Hello sanpai,
Arduino Due, like most of the Arduino boards, it is intended to enable the user to develop applications quickly with the Arduino tools by hiding detail low level stuff.
But, since Due has a different MCU, if compared with its older relatives, I understand your interest to explore Due outside the Arduino environment. Thus, which way?
Given that Due's MCU is the Atmel SAM3X8E, the initial and best platform for exploring SAM3X8E level is the manufacturer's tool itself: Atmel Studio 6.1 which is free and let you download your projects via USB. If you want to grasp deeper inside SAM3X8E, you shall need a debugger like SAM-ICE.
Hey, but SAM3X8E's core is an ARM processor and I want to explore CORTEX-M3 (e.g. Instruction Set Architecture). Yes, Keil could be the way, but MDK-ARM software is an expensive environment (The free version is limited to 32K) and you shall need the ulink2 debugger. Deep waters.
I am telling you, if you only need to download your projects to Due via USB, Arduino IDE remains as your best and free choice. Regards!
Thanks a lot , will dig onto atmel studio 
But, the Keil is very much lighter IDE than AVR studio. if i run avr studio. it will suck half of my RAM. but Keil is not like that. In that i wanted to know whether Arduino Due can be programmed directly without using any extra hardware.
As explained in #1, the free version of Keil is limited to 32kB.
You can use ATMEL-ICE or any of the "debugger-included" Evaluation boards to provide a JTAG/SWD debugger.
Just connect your ULINK, JLINK, ATMELICE, NXP, TI, ... debugger to the 5x2 JTAG header on the Due.
Keil is easy to use and reliable.
There are several Free IDEs e.g. Atmel Studio. Not so reliable but are not size limited.
Personally, I use Rowley with ATMEL-ICE to debug an "Externally built ELF" that was made by the Arduino IDE.
David.