People I have seen generally getting started with Arduino or Raspberi Pi , for programming they use c, python. IOT also has a networking part , for that NS3 can be used!

Cooja is better option

You can explore SimpleIoTSimulator, if your work is based on common IoT protocols

Simulators for IOT

1- Contiki OS + Cooja simulator

As we know, IoT will have various devices and can be divided into different networks. Thus, your security threat model needs to focus a certain level, but not all the levels including hardware, OS, network protocol, and application...The existing answers have clarify the good network simulators you can adopt (Cooja is a cross-level simulator but the others also can run with specific emulators like Qemu and etc).

see:http://www.contiki-os.org/start.html#start-cooja

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2-SimpleIoTSimulator

SimpleIoTSimulator The InternetOfThings Simulator SimpleIoTSimulator™ is an easy to

use, IoT Sensor/device simulator that quickly creates test environments made up of thousands of sensors and gateways, all on just one computer.

System Requirements

64-bit RedHat Enterprise Linux (6.x or higher)

for more details:

http://www.smplsft.com/SimpleIoTSimulator.html

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3- NetSim v9

NetSim v9 (Latest Released Version, Feb 2016)

see this :

Research on Internet of Things(IOT) using NetSim

http://tetcos.com/

https://www.youtube.com/watch?v=ManEw7jXkaw

http://www.boson.com/support/netsim-support-topics

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4- AutoSIM IoT - Internet of Things Simulator

AutoSIM is the worlds first IoT simulator that can simulate 100+ million devices on a cluster of servers and supports 10 protocols below...

SmartM2M

LWM2M

CoAP

MQTT

Automatski (Streamer & Chatterbox)

Rest

Websockets

UDP

XMPP

AMQP

other custom protocols

see this :

https://www.youtube.com/watch?v=VlNIcmP8tvA

.

Regards..

cooja

SimpleIOTSimulator : it is easy to use,IoT Sensor/device simulator that quickly creates test environments made up of thousands of sensors and gateways, all on just one computer.

It includes:

- CoAP

- MQTT

- MQTT-SN

- MQTT-Broker

- HTTP/s client 

HTTPs/server

it enables IoT platform and gateway vendors to improve product quality and significantly shorten their time-to-market without incurring large capital expense for creating test infrastructure.

i use Contiki OS + Cooja simulator

The Contiki OS+ Cooja simulator also  is  highly preferable for the IOT  since it connects tiny low-cost, low-power microcontrollers to the Internet.

As a follow up question, does anyone know which of these simulators mentioned will work best for researching LoRa  i.e Long Range low power internet of things , also widely known as LPWAN.