scholarly journals Gene name errors: Lessons not learned

2021 ◽  
Vol 17 (7) ◽  
pp. e1008984
Author(s):  
Mandhri Abeysooriya ◽  
Megan Soria ◽  
Mary Sravya Kasu ◽  
Mark Ziemann

Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% (3,436/11,117) of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.

2021 ◽  
Author(s):  
Mandhri Abeysooriya ◽  
Megan Soria ◽  
Mary Sravya Kasu ◽  
Mark Ziemann

AbstractErroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.


2020 ◽  
Vol 33 (109) ◽  
pp. 21-31
Author(s):  
І. Ya. Zeleneva ◽  
Т. V. Golub ◽  
T. S. Diachuk ◽  
А. Ye. Didenko

The purpose of these studies is to develop an effective structure and internal functional blocks of a digital computing device – an adder, that performs addition and subtraction operations on floating- point numbers presented in IEEE Std 754TM-2008 format. To improve the characteristics of the adder, the circuit uses conveying, that is, division into levels, each of which performs a specific action on numbers. This allows you to perform addition / subtraction operations on several numbers at the same time, which increas- es the performance of calculations, and also makes the adder suitable for use in modern synchronous cir- cuits. Each block of the conveyor structure of the adder on FPGA is synthesized as a separate project of a digital functional unit, and thus, the overall task is divided into separate subtasks, which facilitates experi- mental testing and phased debugging of the entire device. Experimental studies were performed using EDA Quartus II. The developed circuit was modeled on FPGAs of the Stratix III and Cyclone III family. An ana- logue of the developed circuit was a functionally similar device from Altera. A comparative analysis is made and reasoned conclusions are drawn that the performance improvement is achieved due to the conveyor structure of the adder. Implementation of arithmetic over the floating-point numbers on programmable logic integrated cir- cuits, in particular on FPGA, has such advantages as flexibility of use and low production costs, and also provides the opportunity to solve problems for which there are no ready-made solutions in the form of stand- ard devices presented on the market. The developed adder has a wide scope, since most modern computing devices need to process floating-point numbers. The proposed conveyor model of the adder is quite simple to implement on the FPGA and can be an alternative to using built-in multipliers and processor cores in cases where the complex functionality of these devices is redundant for a specific task.


2016 ◽  
Vol 51 (1) ◽  
pp. 555-567
Author(s):  
Marc Andrysco ◽  
Ranjit Jhala ◽  
Sorin Lerner

2004 ◽  
Vol 39 (4) ◽  
pp. 360-371 ◽  
Author(s):  
William D. Clinger

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