My Research Journey to Brain

This blog tries to summarize my research journey from Universe to Sun to Moon to Earth to Body to Brain.

In school days

[ This blog tries to summarize my research journey from Universe to Sun to Moon to Earth to Body to Brain. Some of this is covered in a talk I gave at IIASA, Vienna – ]

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Use of ICT and Sensor Network Technology in Agriculture in Bihar

Bihar Govt has rightly recognized the potential of agriculture in growth of Bihar. For this purpose a separate “Agriculture Cabinet” has been formed. Road map for agriculture for next 10 years with a massive outlay has been planned as well.

In November and December 2011, I made two visits to Bihar and interacted with Agricultural Research Institute, Farmers and some young Social Entrepreneurs focusing on agriculture. I have also noticed the fact that some of the farmers in Bihar have done world record production of paddy and this encourages me to write this brief note.

In 2011, on behalf of IIT Alumni (Gujarat Chapter) I signed an MOU with Gujarat Govt to “Improve Agricultural Yield using Technology”. I feel that some of the points mentioned in that MOU are also relevant to Bihar. I am willing to work together with Bihar Govt to develop these technologies. The technologies that I am talking about are not part of standard agricultural technologies being covered but are more recent and are under development worldwide. While I would have hesitated to discuss such technologies in Bihar earlier since they would only be beneficial after farmers have started utilizing existing technologies. However now that I have noticed Bihar making fast progress in agriculture, I feel that time is ripe to take up research and development, which would take Bihar to next level and keep it ahead in Nation and World. I would mention these as follows:

Precision farming using sensor network– using the localized sensors linked with wireless communication system to provide real time feedback on various parameters which affect crop yield. As compared to the developed countries, our farm sizes are very small hence we need to develop low cost solutions based on latest advancements in MEMS sensors, micro radio transceivers and processing systems. This would allow us to monitor the spatial variation in moisture, soil properties, hardpan, nutritional status etc. on a much smaller scale.
This kind of technology would allow us to improve the quality of our fruits and vegetables as well as products being developed in green houses. While the basic concept is not new, it is critical to develop such technology at very low cost to make it economical to farmers in Bihar.

Use of Space Technology through Hyper Spectral Imaging– Using the advances in Communication and Remote sensing to create a systematic natural resources database and also to research in the advance area of Hyper Spectral remote sensing to compliment the Soil Health Card Program at ground level.
Soil health card system uses ground level periodic monitoring of soil related information(e.g. every 6 months) based on mobile soil labs to farmers in the villages. This measurement can be supplemented by Hyper Spectral Imaging already available in public domain to provide much greater spatial information and complements the information provided by “Soil Health Card”.

Low cost non-invasive sorting systems – It has now become possible to develop low cost sorting non-invasive machine based on advances in CMOS image sensors and LED light source to sort the agricultural yield based on their attributes such as their quality, size and maturity stage. This would allow farmers to get a better price in the market and would also make it easier for them to access the export market.

Traceability systems development – Traceability is a very important factor in today’s fresh produce industry. With more and more export market coming up with rules for food traceability, it is important to develop low cost technology to meet the needs of food traceability from “seed to plate”.

Traditional systems are very expensive and we need to develop low cost system so that farmers in Bihar are able to export their product in International market, which is going to be crucial for Bihar in next few years.

GIS based planning : Today it has become possible to collect information through remote sensing as well as ground survey using Mobile phones (e.g. Android based systems) regarding crop, water resources, soil condition, weather and all other parameters and add them to a Geographical Information System (GIS) to allow easy access to information and use them in planning. Some of this data can be made available on real time basis through wireless sensor network such as Agro-Weather Sensor Network. It would give a big boost to the way we manage and plan our agriculture.

Embedded Systems through Arduino in Patna

As a way to promote innovation based on ICT, I am planning to organize a 2-day workshop around Feb 20 in Patna. This would focus on “Embedded Systems development using Arduino”. An Aruduino kit would be given part of the registration fee of Rs 3000. This would permit the participant to continue working with the kit at their own and create all kind of things including robots. This would be very useful to college going students, specially Engg students but can be useful to anyone with some knowledge of simple programming. Arduino has been making waves all over the world by bringing benefit of embedded system to non-technical people like Artist/Designers/Musicians … It would be very useful for projects of Engineering students, who can not only use this to make working prototype but also start companies around it. Most of my research projects are done using embedded systems.

If this workshop is successful, I can do more advanced level workshop since I teach 4 semester course on related topics. This can lead to a plan to setup an “Innovation Lab” in Bihar to bring benefit of this to all students and young professionals including school students. In many other parts of India, specially south India, many commercial organizations have flourished around projects but in somewhat unethical manner. We do not plan to take that path but provide knowledge and training to individuals and make available facilities that they can avail of to realize their thoughts and bring innovation in focus.

meshprog failure on Fedora 13/14

While using meshprog on recent distributions of Fedora (13 or 14), I found two issues:

1. One issue is related to gpsd daemon trying to grab the device based on USB-UART converter (e.g. FT232 or cp210x). This is discussed in my earlier post at

Meshprog – USB device opening failure on Fedora 11/12

2. Second issue is related to blocking read used in meshprog code. I found that by making the USB device read non-blocking, it starts to work fine. I am not sure if this is the right way to do it. Here are the specific details:

Go near line 115 in meshprog.c file and change the line to open USB device in non-blocking mode:
// f = open(devicename,O_RDWR);
f = open(devicename,O_RDWR|O_NONBLOCK);

After recompilation, it seems to work fine. I have informed the author of the code.

TinyOS-2.x zigbit serial communication

As mentioned in the previous post, due to the fact that we were downloading the Motorola S-record file ‘main.srec’ via Serial Bootloader (using meshprog on Linux), fuse bits were not getting updated. If we had used JTAG interface (e.g using DRAGON Kit) and aurdude, this would have happened. S-record can have application code as well as fuse bit setting, unlike Intel Hex format.

This meant that the default TinyOS setting of 8 MHz for clock rate was not appropriate for this since Meshbeans are set for 4 MHz by default. So to get the Serial Communication working, we had to make the following changes:

1. Check the following  in


=> change clock rate to 4 MHz by

#define MHZ  4

=> Change here the default baud rate, if you need – 57600 works fine for me


2. make sure that:

“The file chips/atm128/Atm128Uart.h contained some wrong constants, which produce  strange results. The correct ones can be found in the ATmega 1281 datasheet and are:
ATM128_38400_BAUD_8MHZ_2X = 25
ATM128_57600_BAUD_8MHZ_2X = 16”

This change would not have effect on 4 MHz clock that we are using but its best to correct them anyway. Anyother Baud Rate combination can also be added.

I must add here that give a choice use a crystal which gives less errors  – e.g. 3.6864 MHz instead of 4 MHz , similarly 7.3728 MHz instead of 8 MHz. (See the ATMega128a manual).

3. With these changes done, now one can try TestPrintf utility. Do read this README file :

I was first looking at serial data using MiniCom – this was producing some unprintable characters including what is expected. One has to use the Jave client to get the proper message displayed as output of Printf command. I used the following command to get the data displayed right:
java  -comm serial@/dev/ttyUSB3:57600

Here /dev/ttyUSB3 is the port to which my meshbean module was connected vis USB port.

This would give the this  output in a loop:

Hi I am writing to you from my TinyOS application!!
Here is a uint8: 123
Here is a uint16: 12345
Here is a uint32: 1234567890

TinyOS-2.x on Zigbit – Baud rate mismatch

We tried to use TinyOS on Meshnetics Meshbean modules based on Zigbit module containing both microcontroller and radio transceiver. Fortunately a port was made available as a contributed code. I got many student group to start using TinyOS on Meshbean modules. However no one could get the UART communication through USB port working and all the projects which needed this got stalled. I took up this task as I got little free now to figure out what may be happening. It looked like a Baud Mismatch problem since we were received some characters but no baud rate setting was making it come right.

I think I have now understood the problem and however need to try it out tomorrow to make sure that my guess is correct. I am writing it up now and would verify later.

TinyOS port by Distributed Computing Group, ETH used JTAG interface to download firmware into the Meshbean module. This had the capability of programming fues bit as well. What we have been doing is to use Serial Bootloader to program the modules. This does not have the capability of programming the fuse bits. My guess it that due to this the Baud Rates do not match to the right value since clock related fuse does not get set appropriately. I also noticed the default settings of fuse bits are different in Meshnetics software as compared to TinyOS :

Meshnetics : 0xFF, 0x9D, 0x62.

TinyOS : 0xFF, 0x99, 9xE2

So Meshnetics default settings may not work specially since CKDIV8 is the most significant bit of low fuse byte (0x62 vs 0xE2) and can have impact on the clock rate.

I plan to use Dragon to do JTAG programming of Meshbean modules and verify my guess! If it works, we can work on doing Time Synchronization development for seismic measurements.

[Added later : My hunch was correct. Dr Philipp Sommer, who is managing TinyOS port on meshbean also confirmed same. I adjusted some parameters based on his suggestion and it nearly works now. Would update more details in a separate blog.]

Meshprog – USB device opening failure on Fedora 11/12

I had been using meshprog to program Meshnetics Zigbit Evaluation Modules on Linux. I discovered that it was not getting programmed on Fedora 11 or 12. It took me some time to figure out what was happening. I am recording this here in case some one else faces the same problem. Here are my observations:

1. Meshnetics modules use UART to USB converter from Silicon Labs – CP2102. This has idVendor=10c4, idProduct=ea60 as shown by Kernel message.

2. I found that /dev/ttyUSBx to which it was getting attached was not opening by Meshprog

3. System log showed the following :

May 22 20:56:28 ranjan kernel: usb 4-1: cp210x converter now attached to ttyUSB3
May 22 20:56:30 ranjan NetworkManager: <info>  (ttyUSB3): ignoring due to lack of mobile broadband capabilties
May 22 20:56:30 ranjan gpsd.hotplug: gpsd_control(action=add, arg=/dev/ttyUSB3)
May 22 20:56:30 ranjan gpsd.hotplug: socket /var/run/gpsd.sock doesn’t exist
May 22 20:56:30 ranjan gpsd.hotplug: launching gpsd -F /var/run/gpsd.sock
May 22 20:56:30 ranjan gpsd.hotplug: socket /var/run/gpsd.sock doesn’t exist
May 22 20:56:30 ranjan gpsd.hotplug: can’t reach gpsd

4. So it looked like it was trying to attach it as a GPS device by starting gpsd

5. I located the hotplug rule for this and disabled that. In Fedora 11 it s in :


I commented the line :

#SYSFS{idVendor}==”10c4″, SYSFS{idProduct}==”ea60″, SYMLINK=”gps%n”, RUN+=”/lib/udev/gpsd.hotplug.wrapper”

6. Now it works !