scholarly journals Open-source bioimage analysis software to accelerate drug discovery

Author(s):  
Anne Carpenter
F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 302
Author(s):  
Florian Levet ◽  
Anne E. Carpenter ◽  
Kevin W. Eliceiri ◽  
Anna Kreshuk ◽  
Peter Bankhead ◽  
...  

Fast-paced innovations in imaging have resulted in single systems producing exponential amounts of data to be analyzed. Computational methods developed in computer science labs have proven to be crucial for analyzing these data in an unbiased and efficient manner, reaching a prominent role in most microscopy studies. Still, their use usually requires expertise in bioimage analysis, and their accessibility for life scientists has therefore become a bottleneck. Open-source software for bioimage analysis has developed to disseminate these computational methods to a wider audience, and to life scientists in particular. In recent years, the influence of many open-source tools has grown tremendously, helping tens of thousands of life scientists in the process. As creators of successful open-source bioimage analysis software, we here discuss the motivations that can initiate development of a new tool, the common challenges faced, and the characteristics required for achieving success.


2018 ◽  
Vol 34 (18) ◽  
pp. 3238-3240 ◽  
Author(s):  
Anliang Wang ◽  
Xiaolong Yan ◽  
Zhijun Wei

Episteme ◽  
2013 ◽  
Vol 10 (4) ◽  
pp. 417-439
Author(s):  
Alexandra Bradner

AbstractDrug discovery traditionally has occurred behind closed doors in for-profit corporations hoping to develop best-selling medicines that recoup initial research investment, sustain marketing infrastructures, and pass on healthy returns to shareholders. Only corporate Pharma has the man- and purchasing-power to synthesize the thousands of molecules needed to find a new drug and to conduct the clinical trials that will make the drug legal. Against this view, individual physician-scientists have suggested that the promise of applied genomics work calls for a new form of social organization – the open source sharing of molecular probes – in order to speed the generation and understanding of new therapeutics. Recent successes in open source drug discovery show it is possible to produce valuable, empirically adequate, and sustainable collective beliefs without secrecy, proprietary attitudes, initial cooperation from Pharma, or outsized monetary incentives. After reviewing and differentiating these successes, I diagnose the source of this healthy new epistemic strategy.


2006 ◽  
Vol 11 (3-4) ◽  
pp. 127-132 ◽  
Author(s):  
Werner J. Geldenhuys ◽  
Kevin E. Gaasch ◽  
Mark Watson ◽  
David D. Allen ◽  
Cornelis J. Van der Schyf

2014 ◽  
Vol 111 (2) ◽  
pp. S40
Author(s):  
Sean Ekins ◽  
Jill Wood ◽  
Lori Sames ◽  
Allison Moore ◽  
Alex M. Clark

2015 ◽  
Vol 55 (6) ◽  
pp. 1231-1245 ◽  
Author(s):  
Alex M. Clark ◽  
Krishna Dole ◽  
Anna Coulon-Spektor ◽  
Andrew McNutt ◽  
George Grass ◽  
...  

2017 ◽  
Vol 13 (5) ◽  
pp. e1005530 ◽  
Author(s):  
Benjamin Risse ◽  
Dimitri Berh ◽  
Nils Otto ◽  
Christian Klämbt ◽  
Xiaoyi Jiang

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Sandra Duffy ◽  
Melissa L. Sykes ◽  
Amy J. Jones ◽  
Todd B. Shelper ◽  
Moana Simpson ◽  
...  

ABSTRACT Open-access drug discovery provides a substantial resource for diseases primarily affecting the poor and disadvantaged. The open-access Pathogen Box collection is comprised of compounds with demonstrated biological activity against specific pathogenic organisms. The supply of this resource by the Medicines for Malaria Venture has the potential to provide new chemical starting points for a number of tropical and neglected diseases, through repurposing of these compounds for use in drug discovery campaigns for these additional pathogens. We tested the Pathogen Box against kinetoplastid parasites and malaria life cycle stages in vitro. Consequently, chemical starting points for malaria, human African trypanosomiasis, Chagas disease, and leishmaniasis drug discovery efforts have been identified. Inclusive of this in vitro biological evaluation, outcomes from extensive literature reviews and database searches are provided. This information encompasses commercial availability, literature reference citations, other aliases and ChEMBL number with associated biological activity, where available. The release of this new data for the Pathogen Box collection into the public domain will aid the open-source model of drug discovery. Importantly, this will provide novel chemical starting points for drug discovery and target identification in tropical disease research.


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