Faculty Opinions recommendation of Challenges in funding and developing genomic software: roots and remedies.

The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences.However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the research community.I examine the roots of the incongruity between the importance of and the degree of investment in genomic software, and I suggest several potential remedies for current problems.As genomics continues to grow, new strategies for funding and developing the software that powers the field will become increasingly essential.A traveler in late-eighteenth-century England who passed through the town of Slough-located just west of London and not far from present-day Heathrow Airport-might have come upon a massive 40-ft-long telescope, suspended in a wooden frame more than 50 ft tall (Fig. 1a).The telescope was located at the home of William Herschel and his sister Caroline, two of the greatest astronomers of their day.It was the largest telescope in the world until it was dismantled in 1839.Weighing over 1000 lbs., the "40-ft telescope", as it was known, was sufficiently impressive to the general public to emerge as a regional tourist attraction.Its audacious scale inspired prominent thinkers and writers of the time, including Erasmus Darwin and William Blake [1,5].The 40-ft telescope took 5 years to build and was paid for by a grant of £4000 from King George III, who was strongly committed to scientific research throughout his reign.This grant represented a substantial sum at the time, roughly equivalent to £600,000 (about US$800,000) in 2019 [6].There were no formal mechanisms at the time for grant applications for scientific research.Instead, William Herschel simply approached the King directly with a request for royal patronage.The 40-ft telescope is one of the earliest examples of government investment in the infrastructure for scientific research, to enable a project that simply would not have been possible with private funds alone.The model of government investment in scientific infrastructure became increasingly well-established throughout the 19th and 20th centuries, culminating in the "Big Science" of the World War II and Post-War eras.Science in modern times has been dominated, in many ways, by these massive public investments.Prominent examples include the Manhattan project (equivalent to $22 billion in 2016 [7, 8]), the Apollo program (equivalent to $107 billion [9]), the Space Shuttle program (equivalent to $219 billion [10]), the Large Hadron Collider (equivalent $4.8 billion [11]) and, more pertinent to this article, the Human Genome Project (equivalent to $5.0 billion [12]; Fig. 1b).Indeed, we now live in a world where much of the dayto-day work in science depends on a publicly funded infrastructure.In particular, many working in genomics rely heavily on data sets such as those generated by the ENCODE, Roadmap Epigenomics, 1000 Genomes, Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), Genetic European Variation in Disease (GEUVADIS), and most recently, Human Cell Atlas projects.We store and search sequence data using GenBank, EMBL-Bank, DDBJ, UniProt, and Pfam, examine threedimensional protein structures in PDB or EMDB, scour the literature using PubMed, and view genomic annotations using the UCSC Genome Browser and Ensembl Browser.All these resources have been maintained for decades either directly by government agencies or through long-term public funding to universities and research institutes.The computer software on which millions of scientists rely for genomic analysis is no less an essential part of the

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