Imam Samudra is charged with plotting and organising the attacks
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The alleged field commander of last year's Bali bombings has gone on trial.
Imam Samudra is charged with plotting and organising the attacks, which killed more than 200 people - most of them foreign tourists.
If found guilty, he could face the death penalty, under anti-terror laws passed in the weeks after the bombings last October.
Imam Samudra shouted religious slogans as he took his seat at a court in the Indonesian resort island on Monday.
BBC correspondent Rachel Harvey says he was bustled into court with his hands bound behind his back.
Dressed in a pristine white shirt and white prayer hat, he confirmed his identity, giving both his real name along with the seven aliases he has accumulated over the years.
Then for almost two hours he sat quietly listening as the prosecution read the list of charges against him, our correspondent says.
Aged 33
From Tasikmalaya, West Java.
Computer expert
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Prosecutor I Nyoman Dilla read out a 43-page indictment accusing him of planning acts of terrorism, the use of violence to create terror and heavy casualties, plotting an act of terrorism and possession and use of explosives.
Police say he chose the nightclub target and led planning meetings for the attack.
He is also alleged to have stayed behind in Bali for four days after the bombings to monitor the police investigation.
In addition he is charged with organising a robbery to help finance the Bali operation, and of involvement in an earlier series of bombings in December 2000.
His defence team says the indictment against him is too long and complicated, and that the investigation which led to his arrest was flawed by the presence of foreign police officers.
The trial has now been adjourned until Thursday.
Randall Lee, who lost three members of his family, in the Bali attack welcomed the trial.
"He's obviously the link to whoever is orchestrating these attacks," he told our correspondent.
"There's no place in the world for people like him. He should be just taken away and shot in the back of the head and thrown in a ditch," Mr Lee said.
Jemaah Islamiah
Imam Samudra is the second of more than 30 suspects arrested in connection with the Bali bombings to go before the courts.
The trial of Amrozi bin Nurhasyim, who is accused of buying the explosives and bomb-making material used in the attack, began last month and was also scheduled to continue on Monday.
Many officials have blamed the Bali attacks on the militant Islamic group Jemaah Islamiah (JI), but the indictment against Imam Samudra makes no mention of the network.
The alleged head of JI, Abu Bakar Ba'asyir, is being tried separately on charges of treason relating to church bombings in 2000 on the Indonesian island of Batam near Singapore.
Imam Samudra testified in his trial on 28 May.
In his testimony, Imam Samudra denied any connection with JI, but he did admit he was involved in the church bombings.
He said Abu Bakar Ba'asyir had never ordered any bombings and dismissed the cleric as out-of-touch and boring.
"It's the age of the internet but he still talks about mysticism while Muslims are being slaughtered," he said.