Chapter 4: Supercomputing Center#

When she went back that night, Qi Min sent the project plan she had written for funding to Mr. Zheng Wenyu's mailbox.

The next day, when Qi Min was using the supercomputer of her school's computing center to continue to run a larger test set with her existing miniature version of the "brain-like body", she suddenly received an email from Zhou Xiaoshan, a researcher in the "Nimbus" supercomputer project of the Chinese Academy of Sciences.

The email told Qi Min that she would be able to go to the "Nimbus" computing center in Fangshan District tomorrow to discuss the use of it.

At this time, Qi Min really wanted to kiss Yan Zhaolan fiercely - sure enough, it was more reliable to be an old friend!

Now this test set doesn't have to run anymore. Qi Min stopped the code on Jupyter to test the learning ability of the brain-like body, and quickly began to go through the code to generate the brain-like body again. She renamed the variables that had been named hastily and hastily named them shorthand for their purpose, and then commented on each piece of code.

Qi Min used her "beautified" code to re-run an ultra-miniature version of the brain-like body with only 16×16×16 virtual neurons, and saved the code after checking and confirming that it was correct.

If researcher Zhou Xiaoshan agrees with her to use the computing resources of "Nimbus", then she can try to generate full-scale 1:512, 1:64, or even 1:8 and 1:1 brain-like bodies. Once she got her hands on a 1:1 brain-like body, she could just scrape together the experimental data and finish her article.

——

The next day, Qi Min got up early in the morning, and took the subway directly to the "Nimbus" computing center without going to school.

The "Nimbus" is composed of a large computing core group, which occupies a separate computer room for heat dissipation reasons, and the upper floor is equipped with a complex and staggered liquid cooling piping system. Obviously, it is impossible for the staff of the computing center to let Qi Min, an outsider, enter the computer room, and even the researchers working in the computing center rarely have close contact with the real "rain clouds".

The place where Qi Min was going was researcher Zhou Xiaoshan's laboratory, and they made an appointment to meet there.

However, when Qi Min went to Zhou Xiaoshan's lab and asked about the graduate students who were working inside, he was told that their teacher was in a meeting. The graduate students in the laboratory didn't ask Qi Min what he was here for, but Qi Min went in and waited for a while.

Qi Min entered their laboratory and found that although it was also a bioinformatics laboratory, it was very different from what she had imagined.

The biggest difference is that there is no division between the laboratory area and the living area. Because bioinformatics research requires very few "wet experiments" to be performed on organisms or biochemical systems, there is no contamination of harmful reagents and microorganisms, so there is no need to separate the bench from the desk. Also corresponding to the characteristics of bioinformatics, everyone in the laboratory had at least two screens and an abnormally large host on their desks, and the air conditioning in the room was turned on, and Qi Min saw from one of the screens that there was no one but still lit that they were doing a large number of two-dimensional Fourier operations of electron microscope photos.

Qi Min found a place where no one was sitting down, and saw a young man wearing Sennheiser headphones next to him debugging the code.

She couldn't help but glance curiously and saw that what he was writing about was an RNA structure prediction tool. In fact, RNA structure prediction is already a relatively well-studied field, and existing algorithms have their own merits, but for a specific type of RNA, it may be necessary to design a suitable special algorithm based on the information it knows.

And this code looks like it was written by this young man himself, because Qi Min has been watching him revise and change for almost ten minutes, and the output prediction array is still a bunch of negative numbers.

It happened that Qi Min had originally written the code for RNA structure prediction, and at this time, he revised it and read it, and quickly found the problem.

"Hmm...... This traversal doesn't seem right. Qi Min was embarrassed to say it to him directly, just sat next to him and muttered.

At first, the young man was wearing headphones and pretended not to hear, so he didn't pay attention to her at all.

Qi Min saw that he was really struggling to tune it like this, so he couldn't help but say: "For the nearest neighbor algorithm (i, n-i) should start from i greater than or equal to 2, and if i is 0 and 1, the principle of hydrogen bonding should be used at most......"

"It's the 'lowest energy' principle." The young man who tuned the code took off his headphones, turned to her and said, "But the experimental method of the initial test value is different, and the two algorithms cannot be used universally at all." ”

"Who said that? The first pair of hydrogen bond assignments does not affect at all. You try it first. Qi Min said to him.

The young man suspiciously added a paragraph of IF, and copied the relevant code from another algorithm that simply used the principle of energy minimum.

After he ran it again, the output matrix was not all negative.

But it is clear that the result is not right either.

There were still too many negative numbers, resulting in a maximum of less than 4, and it was clear that the 30-base linear RNA used for testing could not have formed only one base pair.

"What's going on?" The young man asked her directly this time.

Qi Min leaned in front of the screen and looked at it carefully, and then said while tapping on the keyboard: "You don't add FLAG in your nested FOR statement that compares the maximum value, just add it......"

The code was run again, and this time the output matrix finally looked normal.

The young man breathed a sigh of relief, and was just about to get up from the chair, but Qi Min said, "Hey, this is still not right. IF YOU LOOK AT THE KNOWN STRUCTURE OF THIS RNA, THERE ARE THREE LOOPS, BUT YOUR ALGORITHM CALCULATES THAT THERE ARE FOUR...... Oh, I see, I have to add an IF to prevent invalid pairing, pairings below two bases in a row shouldn't exist. ”

After she added this IF statement, the final RNA secondary structure was finally the same as the known structure.

"Uh...... You're really ......" The young man looked at the image on the screen and unconsciously showed a smirk.

Then he glanced at Qi Min and asked a little strangely, "Are you new here?" I remember we weren't recruiting PhD students here this year – you're a technician? ”

"No, I just came to find Teacher Zhou Xiaoshan for something." Qi Min said with a smile.

"What's the matter?" The young man asked, and then, as if realizing that this question was a bit of an invasion of privacy, he added, "Maybe I can help you with that, too." ”

"Maybe." Qi Min moved away from his screen, "I came to Teacher Zhou Xiaoshan so that I could use the 'rain clouds'. ”

"Oh, that's easy to say." The young man immediately agreed, "If my boss doesn't agree, you can still use my number." ”

"That's still not good......" Qi Min smiled a little embarrassedly. There are a lot of computing resources occupied by running a brain-like body, and if you secretly use a doctor's number, it will definitely arouse the suspicion of administrators.

"What's that?" The young man said indifferently, "The computing power of 'Nimbus' is so strong, and ordinary projects are not a problem at all." The boss just wanted to do something big and test its actual computing power, so he summoned us creatures to come and pick up the work. To be honest, I hadn't learned much Python before I came here. ”

You can see it. Qi Min silently commented in his heart, and then asked jokingly: "Then if Teacher Zhou Xiaoshan rejects me, I will really come to borrow your number?" ”

"Yes, of course." The young man immediately said, "Let's add a WeChat, when the time comes, there will be a bug in this RNA algorithm, and I will have to find you again." ”