Bioinformatics – Optimal Leaf Ordering

For my Bioinformatics project, I, with the help of Dr. Ivaylo Illinkin,  designed a program that takes a bunch of numerical sequences (i.e. a list of lists), and orders them – the lists in the “bigger” list – on the basis of their closeness (measured in terms of their distances) amongst each other. This project was based on a paper by Ziv B. J. et. al. entitled “Fast Optimal Leaf Ordering for Hierarchical Clustering”. The basic algorithm for the program was to generate a leaf cluster using the UPGMA algorithm, followed by finding the leaf order that carries the minimum calculated distance score with particular leaves on the very first and the very last position of the list. The algorithm checks all the possible combination of the leaves generated from the UPGMA clustering and therefore runs in O4 time space.

Here is a demonstration of what the program actually does.

optimal leaf ordering example

 

Please visit this site on Optimal Leaf Ordering to learn more what the program or use the program itself.

Free Bawo / Bao / Omweso African Mancala Game on www.bawogame.com

Fumba Game Labs™ will be officially releasing its first version of the traditional African mancala game on the 8th of August, 2010. Bawo ( Bao, Omweso ) is played is several countries of Eastern Africa (including Tanzania, Kenya, Malawi and eastern Congo) but it is most popular among Swahili people of Tanzania and Kenya. [ref: Wiki].

Fumba Game Labs™ Bawo Version 1 will be available for free download at http://www.bawogame.com . The bawo game will be compatible with all Windows Operating Systems (XP, Vista and 7), Macintosh OS and Mobile Devices that support Adobe Flash Player. The game will also be playable on Apple iPhone and iPad.

The first version of FGL™ Bawo Game will be available as a standalone application which will not require any installation. It will also be playable online from any browser with the Adobe Flash player plugin.

Fumba Chibaka*
Game Designer, Fumba Game Labs™.

The game link is www.bawogame.com.

[*Fumba, friend of mine, is finishing up his Bachelor’s Degree in Computer Science from Gettysburg College. For more info: http://fumbani.blogspot.com]

The last gaze

a fireI had never seen my brother in tears before. I could not tell if he was really trying to balk his tears, but his eyes were thick with them. Although he was squatting on a greasy rock a few steps behind everyone, he was stealing every last remains of my grandfather through the crowd. Everyone at the cremation was standing around this mammoth fire eating up the last of the woods and my grandfather. The wood blended and merged with his body like the red and orange in the fire.  His right arm that had crept out of the woods looked like logs – all thick, all voicing their recent fate through the deep, pulsating red. The fire was growling in that dusky wind, and Ghatko khola – the river passing through Panauti – was roaring its mourn below the rocks.  Panauti had lost an educational, social and cultural protagonist, a freedom fighter.

Mira’s trip to the well

In the midst of such dysfunction, function is necessary. That is what Raju would have said. His voice still ringed deep in her consciousness, as she climbed down the muddy staircases down the hill in that hot sunny afternoon. The white clouds were misty and slowly dancing around up in the sky, but she was sure they would dare not meddle with the sun up in her village and down in the well she was going to. The ‘staircases’, she noticed, had lost their structure in some places – it must have to do with the haphazard scramble-up-the-hill moves the Maoists had been forced to last night. The grasses, on the sides, were also uprooted at some places. She found a chunk of grass uprooted in one of the bends downhill, and put her gagri* down by the path and bent down with the hope that she would be able to see one of the bullets. The mud was dry and wet. The grass, green and shiny. She poked her finger around the hole. She even bent over to see if she could find any hole that will ease her search. But she didn’t see anything. Tired and unsuccessful, she bent back and leant against the terrace to see all rice paddies and the beautiful trees down by the river and her friends’ house way in the distance. The sun is really on today, she thought, as she laid her feet flat on the path and soaked up the heat while trying to rip up some of the grass beside her.

“Mira! What are you upto?” she heard.

“Oh, Ram daju*! I was just enjoying the sun a little bit. How are you doing today?”

“I am okay. I just wanted to see how my daughter is doing.”

“Oh. Ramila didi* is fine. I met her earlier while I was getting ready to cut the hay for the cattle. She said that Ravi and Raghav were crying all night long. I couldn’t sleep way till the morning myself,” she said.

“Neither could we! We could hear the gunshots and that blast. That even shook our house. I am pretty sure the police station is all up in smokes now.”

“I guess so. My brother used to say that that would be the first thing he and his friends would go after. I thought he’d stop by the house last night. But, I guess not when there are bullets flying everywhere. Our front wall has two of such bullet-holes. But I just hope that Raju’s not hurt.” She added, “But yeah. I am not sure how many people died in the attack. Papa said that the Maoists took all their casualties in big baskets and sacks, and that there are only like three policemen who are really hurt.”

“So, technically, no one knows how many are dead?”

She slightly nods her head in affirmation.

“Ok, I guess, I will go meet Ramila now. I will see you later Mira.”

“See you Ram daju!”

Mira could feel her feet soaking up the heat. Up in the sky, however, the clouds were mischievously getting closer to the sun which was itself trying to hide from her behind the tall trees up in the hill.  She scrambled herself up, dusted off the back of her kurta*, and continued her journey down holding the gagri by the fingers.

The well was down at the foot of the hill, with the trees giving it a very cool shady feel. As she got close to the water, and dipped her gagri down in the water, she noticed that the water looked very unusual and different. In fact, against the bright tingles in her eyes, she could tell that it looked a little red. Then, she got scared. She blinked hard and fast trying to wash the tingles away. When she tried to gaze at the water again, she saw it: a dead body – flat on the ground just by the water. She couldn’t see the face, but she could see that his left arm on top of the bamboo stump was red and had blood dripping all the way down to the fingers and onto the water. Although, she wanted to freak out and run, she walked around the water close to the body. The left side of the face was flat on the mud; but thankfully, from the other half, she knew that it was not her brother. She didn’t know who he was. But, she couldn’t stand the sight any longer. She turned back, grabbed her gagri and then ran up the same path she came from.

She still remembered telling Raju not to join the Maoists. “Think about your family,” she had said. “What would dad do without you? We don’t want to lose you.” She knew what Raju was going to say: “My country is my family now. My brothers here in the village and the towns afar need my support. We have had enough with this shitty government. Ever since there has been democracy here, people are getting poorer and the bureaucracy is rotting every minute. We need communism. I cannot watch my brothers suffer and die alone. I have to help them. You will see the change yourself sister, come 10 months.” It hadn’t even been more than three months that she last heard those words from her brother. She was getting scared as she swiftly climbed the muddy staircase to tell her father of what still remained of the terror last night.

As she scrambled her way up the hill, she saw a procession of soldiers, in their typical camouflage outfit and helmet and what looked to Mira like M15A4 machine guns walking down the hill. Raju had showed her one of those guns only a couple of weeks ago. Among many things that night, Raju had said that that gun was going to be his best friend from then on. As soon as she saw the armies, she slowed down. But as she pressed against the terrace to make a way for the soldiers asked her why she had been running. Mira, feeling nervous and insecure, told them of what she saw down by the well. The armies then walked faster to the well.

As she scooped some final steps up and onto the small space in front of her house, she saw her father sitting on the side door. She knew he had finished cutting the wood, and was waiting for her to bring some water and get the food ready. But, as Mira walked towards her father tired, with the gagri hanging loose in her hand, he asked, “What happened? Are you okay?” After she caught her breath, she recounted all that she witnessed. After some time, his father looked sideways, then whispered, “Mira, your brother is here”, and then directed his head to the door. Mira, all of a sudden excited and anxious, walked into the house, (and saw his brother sitting on the foot of the ladder right next to the door. )

“Hey sister,” he said. “I was just listening to your story. How are you?”

“Me? You’re asking about me? Look at yourself. You’ve changed so much!” she said as she looked at his muddy boots, stubby cheeks and his red and white Maoist scarf wrapped around his head.

“You don’t have to wear that scarf in here. In fact, you don’t have to wear it at all. Why would you flag yourself around like that? You don’t -”.

He then showed his band on his right wrist.

“What is it?”

“It’s a band. It means that I am the new commander of my squad. And we have a rule that unless it is a life-threatening situation, we, the commanders, have to keep this scarf on,” he replied.

“Bull shit. That’s nonsense.” Mira said. Leaning against the door, her father started smirking.

“What?” she frowned at her father.

“Sister, I don’t have time to fool around. I have a friend with me upstairs. If you don’t mind, can we get some food?”

“O. Let’s go up then. But I am afraid, I don’t have much water left.”

“Oh. Don’t worry about that. We always carry these around,” he said holding his aluminum bottle for her to see. “Hopefully, he still has some water left.”

Up in the kitchen, Mira got the food ready for all four of them. As they sat in line on the sukul*, she remembered that she left the gagri down by the door.

“I think I left the gagri downstairs. Let me go get it. You guys can start eating. I’ll be back in a minute,” she said.

As she walks down the ladder, she hears a blast. It was loud and ominous, and instantly reminded her of the incident again. Then she heard a couple of gun shots. She had a feeling that they all were coming from down the hill, probably somewhere near the well. As she ran down the ladder, some more shots crack the silence. She then quickly closed the front door, and went into the room opposite to check if all the windows in the shed were closed.

“Mira! Why are you lingering in there?” she heard her father speak.

“Wait!” she said, as she closed the last window. She heard some more shots reverberate in the shed, while the cows started mooing and showing their discomfiture by walking left and right and sometimes, pulling the ropes taut. She closed the door to the shed and swiftly walked up the ladders. As she reached the kitchen, she saw her father, eating all by himself. She noticed that the room had an eerie feeling, with the window half closed. Both her brother and his companion had left their plates with just some rice mixed up with the curry on the side. “Where are they?” she asked.

Her father directed his head to the window. “I told them to wait. They didn’t listen.”

************The End*************

Legend:

*gagri = It is a special type of water urn, that (Nepalese) women use to carry water around.

*daju = a Nepali word for brother (not necessarily own relative)

*didi = Nepali word for sister

*kurta = a special light outfit worn mostly by women in Nepal. (Men also wear them in the south of the country and in India).

*sukul = a mat made out of straw (used a lot by the people in the villages in Nepal).

Crazy Zipper!

Jeans_zipper_closeupImagine yourself sitting in a box shaped like a giant whistle. You have your legs blocked by a sturdy strap, and you have bars to hang by all your might. The box, attached to a giant rod, can spin freely on its hinge. What happens when the giant rod starts spinning? Your nightmare!

Fumbani ( mi amigo, Mr. Mzuzu from Malawi) and I were crying loud enough to muffle every other  freight voiced similarly in other boxes. Never in my entire life had I felt so much of force; my back was completely  against the back of my seat, alright – but my belly was experiencing the g-force in agony after a while. Needless to say, this was making me feel as if I was being shot out, along with the box, into the space, far away.

But this was just a cast. I started really freaking out when the spin shared the frenzy with the g-force. One swift 360 up in the air – my hands clinging to the bars as strongly as my larynx was working – followed by another one – all while the things down below were zooming on and off. “Dinesh, make them stop. Make them stop”, Fumba said with his face hunched down, a mobile in his right hand recording our frenzy cries all along. “They are stopping”, I said and wanted to believe. But, whoop! every thing started spinning on the reverse, and then everything repeated again; “oh my god! Oh my god! Oh my god!”, and ‘the reverse 360s’.

zipper

After we were out, Mr. Mzuzu stopped to record an outsider’s view of what we experienced. I looked at it too, with a weird sensation ringing in my gut. As I looked, all those whistle-shaped-boxes started spinning and moving along a rod spinning in itself-giving an impression of a giant zipper. As I feel my breath scathe my windpipe, I am thinking – obviously, the crazy zipper did everything to us, but zip our mouth shut.

As if it was not enough, we went for the ‘Orbitz’, which was as bad, if not worse than Zipper. We were experiencing the “fictional” centrifugal force, upto its maximum craziness. Just to give you an idea, my lips were flapping over half the ride, while my arms were tight against the side of my seat almost throughout the ride.