nycdaug Chapter 51 First Steps into the Laboratory
Chapter 51 First Steps into the Laboratory
next day
On the third floor of the biology laboratory building at Jiangcheng University, the corridor was filled with a faint smell of disinfectant.
Hu Biao stood at the door of the "Data Analysis Room for Functional Evolution of Non-coding RNA in Complex Diseases" and gently knocked on the open door.
The data analysis room is large and divided into several areas. Along the wall are rows of sequencers and high-performance computing servers with flashing indicator lights of various colors; in the middle are several long experimental tables with equipment such as centrifuges and PCR instruments; at the far end is a small meeting area with whiteboards covered with complex formulas and pathway diagrams.
The four people were discussing something in the meeting area when they heard a knock on the door and turned around at the same time.
"Excuse me, which one of you is Senior Sister Qin Yu? Dean Shen sent me here..." Hu Biao began.
"You must be Hu Biao?" One of the pretty girls in the group stood up. She looked to be in her mid-twenties, with a neat ponytail, delicate features, and wearing a white lab coat over a simple beige cardigan. "I'm Qin Yu. Teacher Shen already told us about this yesterday. Welcome to the analysis team."
A young man wearing black-rimmed glasses and with slightly messy hair also reacted. He was about twenty-seven or twenty-eight years old, tall and thin, wearing a plaid shirt and jeans. He stood up and smiled at Hu Biao, saying, "I'm Chen Haoran, and I'm also Professor Shen's doctoral student. I mainly do bioinformatics analysis, especially sequence alignment and functional prediction."
The other man, who looked a bit older, around thirty, was slightly overweight and wearing a dark blue polo shirt. He had a gentle smile: "Zhou Mingyuan, a postdoctoral researcher, is responsible for the overall data integration and project management of the research project. Our project is a university-industry collaboration between Jiangcheng University and Ruikang Pharmaceutical."
The last woman appeared to be the most mature, around thirty-four or thirty-five years old. She wore a well-tailored dark gray suit and exuded a capable air: "I am Li Wei, a senior researcher in the Bioinformatics Department of Ruikang Pharmaceuticals, responsible for bridging the research findings of my research group with the company's drug target screening efforts."
Hu Biao greeted everyone with a smile, gaining a preliminary understanding of the data analysis lab. Qin Yu was responsible for generating data from upstream experiments, Chen Haoran was responsible for core analysis, Zhou Mingyuan coordinated the overall process, and Li Wei represented the investors and utilized Ziyan's resources for certification.
"Junior Hu Biao, I finished reading your paper last night. I was just about to verify it today, and you showed up just in time. That's great! By the way, are you sure you're a freshman now?!" Chen Haoran said half-jokingly.
Hu Biao smiled helplessly.
The other people in the lab laughed too, and then there was an awkward silence.
They're all STEM students, and they're not young anymore, but their social skills haven't improved much.
"Alright, everyone, stop joking with the junior. Chen Haoran, why don't you show him around the lab and introduce us to our work? Perfect timing, isn't he good at data deconstruction and analysis? Let him share your workload. This is also the teacher's idea," Qin Yu said. As the youngest, she was the one in charge of the data analysis lab.
"Great!" Chen Haoran had no complaints about this; on the contrary, he was very happy. Data analysis is really troublesome, and he was glad to have someone help him with the analysis.
"Actually, our lab is only part of the research group. Our main task is data analysis and comparison..." Chen Haoran led Hu Biao on a tour of the lab, and finally came to his workstation. Pointing to the empty space next to him, he said, "The data analysis room isn't big, but we don't have many people either. You can choose any of these workstations."
Thank you!
Hu Biao thanked him, chose an empty seat, put down his backpack, tidied up his things, and turned on his computer.
"Junior brother, give me your email address, and I'll send you the data and requirements that need to be analyzed. If you don't understand anything, just ask me."
"Okay!" Hu Biao nodded, gave his email address, received the data, and then looked at it carefully.
What can a freshman who just joined the analysis team do on his first day?
Of course, the first thing to do is to familiarize myself with the analysis room.
After watching for half an hour, Qin Yu suddenly pushed a whiteboard to the center of the laboratory and clapped her hands.
"Alright, everyone come over here. The control group just sent us a set of data that needs analysis urgently. Everyone, please take a look!"
As Qin Yu spoke, she wrote on the whiteboard with a pen. Before long, the whiteboard was covered with rune-like mathematical symbols and data. "This is a set of long non-coding RNA sequences associated with neurodegenerative diseases. These sequences have extremely low conservation among different species, but clinical data strongly suggest that they may play a regulatory role in the development of the disease."
"The problem is," Qin Yu pointed to a series of sequence alignment images on the whiteboard, "that using traditional tools like Clustal Omega and MAFFT to align them results in a complete mess. Highly variable regions are completely unalignable, let alone identifying potential functional modules."
At this point, Li Wei added, "The company hopes to identify several promising targets for preliminary screening before the end of the year. If we can't even pass the sequence alignment stage, subsequent conservation analysis, secondary structure prediction, and interaction network construction will all be out of the question."
Chen Haoran looked at the contents of the whiteboard, raised an eyebrow slightly, and turned to Hu Biao, saying, "Junior brother, take a look at these sequences and see if they are suitable for the multi-sequence comparison algorithm you proposed. I remember there was related content in your paper."
"Uh, this..."
"Make way, everyone make way, let our junior brother show off!"
Zhou Mingyang, standing to the side, shouted excitedly.
Hu Biao was a little confused. Looking at the chaotic sequence on the whiteboard that resembled a cryptic script, he smirked and said, "Showing off? What a joke! I'm only a freshman. Do you think I can pull off something like this? Just modeling this kind of sequence would take several days..."
"Haoran, what do you think?"
Chen Haoran shook his head. "These sequences vary greatly in length, and we can't prune them arbitrarily because we don't know the pruning threshold. It's very difficult to control the degree of pruning. If we prune too much, we risk losing functional regions; if we prune too little, we won't solve the fundamental problem. Junior brother, I'm not joking. Your multi-sequence comparison algorithm might be helpful, but I haven't fully grasped it yet. There are some parts where I'll still need your help."
"Haoran, it seems you have an idea?" Qin Yu asked, as if she had noticed something.
"It's not really a line of thought," Chen Haoran said, standing up and walking to the whiteboard. He picked up a marker and started drawing on the blank space. "It was inspired by my junior's paper. If we use dynamic programming combined with an entropy weight model, we can design an adaptive threshold. Simply put, instead of fixing a length or complexity threshold, we let the algorithm dynamically decide which regions need to be focused on and which can be treated relatively leniently based on the characteristics of the local sequence."
He quickly outlined a simple algorithmic framework: "For example, here we can introduce a weight function based on local information entropy. In regions where the sequence is highly variable, we reduce the weight of strict alignment to allow for more gap insertions; while in relatively conservative regions, we increase the weight to ensure the accuracy of the alignment of core functional modules."
Qin Yu's eyes lit up: "This is equivalent to adding an attention mechanism to the algorithm, letting it know where to focus?"
"That's one way to understand it," Chen Haoran nodded. "However, to implement it, we need to embed a weight adjustment term into the core recursive formula of dynamic programming. This will require your help, junior brother. After all, you wrote the paper, and you understand some of the underlying ideas best."
"Then let's give it a try!" Hu Biao said with a wry smile.
Now that things have come to this point, there's no way to refuse.
Over the next few hours, Chen Haoran helped him configure the computing environment, Qin Yu provided the data access path and metadata description, and Zhou Mingyuan coordinated the priority of server resources.
Hu Biao finally witnessed the workflow of a real biological laboratory.
Regardless, the gains were still significant.
In the afternoon, just as he was discussing algorithms with Chen Haoran, his phone vibrated. He glanced at the screen and saw it was Lin Wanqing.
"Excuse me, I need to take this call." He walked to the corridor outside the laboratory.
As soon as the call connected, Lin Wanqing's aggrieved and angry voice came through: "Hu Biao! Where are you now? You've ruined me!"