Technology meets archaeology to decipher early human civilisation

Inspur Information has partnered with China’s first ancient DNA laboratory (known as “The Lab”) to apply intelligent computing to archaeological research in ancient DNA. This union of modern technology and ancient history helps to unveil the myths of ancient creatures, uncover the evolution of ancient cultures, and trace the origin of human civilisation with a cross-disciplinary, cross-cultural perspective.

“Who are we? Where did we come from? Where will we go? Human beings are constantly searching their own past and the path to the future. Archaeology is the tool that humans employ to peer through the sand of time and look back into their own history,” says Liu Jun, VP and general manager of AI and HPC, Inspur Information, “Inspur is launching the “Computing for Good” initiative in pursuit of a truly inclusive world of science and technology. Inspur firmly believes that science and technology will make the world a better place to drive industry progress and achieve social innovation.”

Technology empowers archaeology to discover more possibilities of human origin

Since the third technological revolution, the application of technology in archaeological research has dramatically enhanced its precision. For instance, in the field of molecular archaeology, technology has enabled researchers to extract and analyse the DNA stored in ancient remains. Coupled with interdisciplinary research, archaeological research has become more precise, scientific, and objective.

Through interdisciplinary research that combines archaeology, anthropology and linguistics, the Lab has made significant contributions to the traceability of ancient human DNA, ancient plant and animal DNA as well as ancient civilisations.

In 2019, The Lab successfully deciphered the whole genome of the world’s first ancient wheat, which provided direct chronological evidence for understanding cultural exchanges and agricultural communication between the East and West. In 2020, the laboratory research results revealed population interactions in northern China since the Neolithic Agricultural Revolution, providing important evidence for exploring the origin, formation, and development of Chinese civilisation.

Advances in science and technology have provided new resources and tools for the study of ancient civilisation, helping archaeological research to leap from qualitative to quantitative, making research results more accurate as well as providing unlimited opportunities to approach the truth of history.

Computing power to unlock the secrets of ancient DNA

Ancient DNA uses scientific methods to simulate the evolution of civilisation, allowing us to survey objects from magnificent mountains and rivers down to the minuscule microbe. However, compared to modern DNA, ancient DNA research still faces many difficulties.

Ancient DNA is shorter than modern DNA due to its age, hydrolysis, oxidation, and microbial degradation. On the other hand, ancient DNA sequencing is also more complex because there is a larger amount of data that must be read and compared, which first needs to be cleaned and processed before sequencing.

The methods used to increase the reliability of results — making the sequencing Mosaic more diverse and repeat more times — lead to extremely large sequencing datasets. Ancient DNA research has achieved the development and application of high-throughput sequencing technology platforms and an enhanced ability to capture small fragments of ancient DNA molecules. This is an important breakthrough that addressed previous research problems due to lack of data but has created new challenges in DNA data processing.

A leap in gene sequencing speed — 39 times more efficient

In collaboration with Inspur Information, The Lab developed a gene sequencing acceleration program that sped up the identification and analysis of ancient DNA. The entire genome analysis can now be completed in only 9.64 hours, and the entire exome can be completed in just 48 minutes. Group analysis and genetic data processing speed increased 39 times compared with the CPU-based program. The solution provided by Inspur accelerates the preservation and analysis of ancient DNA data, maximises the accuracy of sequencing, improves the use efficiency of ancient DNA, and speeds up the results of ancient DNA research.

Inspur’s computing solution leverages field-programmable gate array (FPGA) accelerators to solve the challenges posed by ancient DNA. The solutions with FPGA accelerators are programmable, enable parallel computing, and provide low latency, delivering powerful acceleration for AI and HPC scenarios such as gene sequencing, voice recognition, video processing, and risk management. After rigorous testing and comprehensive assessment, The Lab decided to work with Inspur to apply the FPGA technology into the gene sequencing of ancient DNA. This collaboration marks the first gene sequencing with FPGA accelerators in the field of ancient DNA research in China.

The new gene sequencing solutions use the Inspur F10A FPGA accelerator as the core computing unit and are integrated with the Falcon GATK (Genome Analysis Toolkit) gene processing software. In a half-height, half-length form factor, the F10A is the highest density FPGA accelerator with the most powerful performance that supports OpenCL (Open Computing Language). Its small power consumption of 35W is suitable for various complex computing environments such as data centres, edges, and desktops. With a performance of 42GFlops per watt, Inspur F10A can easily support a professional software algorithm library.

The integrated GATK gene processing software of Falcon is fully consistent with standard bioinformatics analysis tools, including all workflow of GATK Best Practices, such as BWA, Picard, and GATK. The integrated software is identical to the original software with the same command. Users can easily use and adjust the data because of the intermediate data which is consistent with original samples.

At present, based on the new accelerated computing system for gene sequencing, researchers in The Lab are analysing the bones of the nomads in the northern Chinese grasslands, such as the Xiongnu, Donghu, Xianbei, Wuhuan, Khitan, and Mongolia as well as unearthed animals and plants for DNA extraction and research. They are also leveraging the research results to learn about the biological relationships between the ethnic groups along the ancient “Silk Road” in Xinjiang, the migration and intermingling between the people, economic and cultural life, the natural environment, and the relationships among people, etc. Such research continuously provides new material for ancient history, culture, and ethnic research, and opens up new horizons.

With the power of computing, Inspur is helping archaeology achieve spectacular breakthroughs in speed, breadth, depth, and precision. Empowered by Inspur’s purpose of computing for good, the ancient DNA laboratory (The Lab) is one step closer to uncovering the origins of human civilisation.