Send APDU commands to USIM/SIM card in android

Starting on API level 22 (Android 5.1) there is another Option called "Carrier Privileges". It allows non-system apps to send APDUs to the SIM card using Android TelephonyManager. See: https://developer.android.com/reference/android/telephony/TelephonyManager.html#hasCarrierPrivileges()

For example mobile network operator (MNO) Apps that are distributed on Google Play can use this. But again it's not open for everybody. In this case you need to be granted access by the SIM. The Access Rules on the SIM are managed by the MNO who issued it. See also: http://source.android.com/devices/tech/config/uicc.html

There can be two different types of applets present on your SIM card.

Common applets

Common applets written in plain JavaCard. This is the type of applet you are used to from the world of common smart cards. It has the process method and smart card is the passive subject in the communication: your app sends APDU commands and the card responses.

You can communicate with these applets using a special set of Android libraries called SEEK for Android. Have a look at this tutorial to learn how to create such a phone application.

Starting on API level 21 there is also a way to communicate to SIM using Telephony Manager. However, there is one huge obstacle: your app needs MODIFY_PHONE_STATE permission, which can be granted only to system apps. A reqular, non-system app isn't allowed to use it.

SIM Toolkit Applets

A SIM card is much more than just a common smart card and writing an applet for a SIM card can be much more complicated than for a common smart card if you want to use all the possibilities the SIM card offers. I recommend you to read this paper - it is someone's bachelor thesis, but it is the best overview for a beginner I have found all over the Internet. I also recommend this video from the DefConn conference.

The role of the applet loaded on the SIM card is different: the applet is no longer a passive entity. The phone asks your applet regularly: "Is there anything new I can do for you?" and your applet can reply: "Yes, send this SMS, please" or "Tell me what time it is" etc. Moreover, your applet can become a listener of some events: incoming call, received SMS, time interval elapsed etc. Yes, the SIM card seems to be passive from the technical point of view, but its role is in fact an active one: it is the SIM card who sends commands to the phone.

These commands are called "proactive commands" or SIM Application Toolkit commands. Structure is the same - CLA INS P1 P2 LC data LE; the meaning is different.

You can send them from your applet using classes in a special JavaCard package called sim.toolkit.

(SIM Application Toolkit is a standard that specifies the proactive commands in the same way Global Platform specifies the applet's lifecycle.)

Example of SIM Toolkit applet:

import sim.toolkit.ToolkitInterface;
import sim.toolkit.ToolkitRegistry;
...
import javacard.framework.ISOException;

public class STKTest extends Applet implements ToolkitInterface {

public static void install(byte[] bArray, short bOffset, byte bLength) {
    // GP-compliant JavaCard applet registration
    new STKTest().register(bArray, (short) (bOffset + 1), bArray[bOffset]);
}
//this method handles standard APDU commands
public void process(APDU apdu) {
    // Good practice: Return 9000 on SELECT
    if (selectingApplet()) {
        return;
    }

    apdu.setIncomingAndReceive();
    final byte[] buf = apdu.getBuffer();
    switch (buf[ISO7816.OFFSET_INS]) {
    case (byte) 0x00:
        //do something
        break;
    }
}
//this method handles the SIM Toolkit commands
public void processToolkit(byte event) throws ToolkitException {
    switch (event) {

    case ToolkitConstants.EVENT_TIMER_EXPIRATION:
        //do something
        break;
    }
}

}

Yes, you should learn Android - you will need it to use the SEEK library. Your question is very broad, please ask me for any details, if you want.