The Role of Digital Notebooks in the Brave New World of Genomic Science

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digital notebooks
Analyzing genomic data is a complicated endeavor, but the process of collecting and analyzing these data could be made easier with digital notebooks.
Image Source: Flickr user Jer Thorp

Not too long ago, sequencing the human genome “was one of the most ambitious projects ever attempted.” Today, scientists have sequenced the genomes of hundreds of creatures throughout the sky, soil and ocean, in our bodies and from our diseased cells, such as cancers. Today, for less than $100 a person can have his or her entire genome sequenced by a number of private companies.

In this brave new world of genomic science, researchers and physicians have begun to talk of science’s next big innovation, namely the field of personalized medicine. According to the FDA, personalized medicine, also known as precision medicine, will enable “the tailoring of medical treatment to the individual characteristics, needs, and preferences of a patient during all stages of care, including prevention, diagnosis, treatment, and follow-up.”

In order to provide such tailored medical assistance, an individual’s genome will take center stage in his or her care. Indeed, it is the sequences of As, Ts, Cs, and Gs that make up our genomes that also determine how likely we are to react positively to one medication and negatively to another. The genome serves as an instruction manual for the creation of our cells and proteins, which in turn determine how we respond to the environment and subsequently, medical interventions.

And this brave new world is now in some fields. Already the identification of genes linked to breast cancer (BRCA1, BRAC2) have enabled women such as actress Angelina Jolie to make decisions about their preventative care. The anti-cancer drug Cetuximab is known to work remarkably well for some individuals, but not in those with a genetic mutation known as K-ras. This knowledge allows oncologists to make important decisions about patient treatment.

However, there is a “problem” to consider with these huge leaps in progress. Ambitious scientific and medical endeavors have taken biology into the “world of big data,” which is “generating data at crushing speeds.” “The life sciences,” in the words of Eric Green, director of the National Human Genome Research Institute, “are becoming a big data enterprise,” and are thus accumulating the problems of big data, which include questions about how to interpret the data, which pipelines to use, what is significant or not and how can we generally make sense of everything.

Digital notebooks to the rescue?

In order to organize this information, genomic scientists need not only their sequencing machines and sequence analyzers, but a careful method in which to store what could be hundreds of gigabytes of information. Beyond data storage, this information must also be searchable and easily found when needed. Given these necessities, a digital notebook should absolutely be a part of the toolkit for any genomic scientist. And there are three more reasons why:

  • Collaboration with security: Digital notebooks are a significant improvement over paper lab notebooks, but more so digital notebooks allow researchers to collaborate effectively with one another. Thus, as sequencing results are analyzed, comparisons can easily be made between companies and the data interpreted by different people in order to facilitate the process of deciphering what are often very large datasets in a timely fashion. Additionally, digital notebooks are IP protected and highly secure, enabling scientists to collaborate without compromising the integrity and privacy of genomic data. Given that timestamps are used whenever an individual logs in and all edits are recorded, this provides additional security that any information stored on a digital laboratory notebook will not be stolen or tampered with.
  • Simplification and streamlining of record keeping and data acquisition: Computer programs are used to sequence genetic material; however, digital notebooks can streamline this process by directly downloading acquired data into the digital notebook format. This information can then be accessed remotely by scientists who can begin the necessary data analyses. Also, pre-designed templates constructed specifically for a genomic scientists can further streamline the process of analyzing genetic data, while also giving scientists the opportunity to record important notes, additional data or experimental conditions that should be considered for a given dataset.
  • Posterity: Each year, millions of gigabytes of data are generated by genomic scientists and though an individual lab might not see this amount of data, there are still significant amounts of data created. Storing this information in a way that maintains the integrity of the data becomes a significant challenge and cloud-based digital notebooks can provide a way forward. If not all data can be stored on these servers, at least some of the data can, thus providing researchers with greater flexibility in the management of their information.

Digital notebook technologies have developed rapidly in the past decade and as big data comes to overwhelm a number of scientific disciplines, ways in which to maintain good records, secure information and facilitate data access become increasingly important. Digital notebooks thus provide an important way forward. To find out how the BIOVIA Notebook can impact your research, please visit our website today.

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