Challenges in funding and developing genomic software: roots and remedies
Author:
Open Access
- 29 July 2019
- journal article
- research article
- Published by Springer Nature in Genome Biology
- Vol. 20 (1) , 1-14
Abstract
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.Keywords
Funding Information
- National Institute of General Medical Sciences (R35-GM127070)
This publication has 141 references indexed in Scilit:
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsGenome Biology, 2013
- Discovery and characterization of chromatin states for systematic annotation of the human genomeNature Biotechnology, 2010
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- Multiple Alignment of DNA Sequences with MAFFT2009
- A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated IndividualsThe American Journal of Human Genetics, 2009
- A new multipoint method for genome-wide association studies by imputation of genotypesNature Genetics, 2007
- Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 2006
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. ThorntonJournal of Molecular Biology, 2000
- Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology, 1997