DRfit : A Java tool for the analysis of discrete data from multi-well plate assays
- Hofmann, Andreas, Preston, Sarah, Cross, Megan, Herath, Dilrukshi, Simon, Anne, Gasser, Robin
- Authors: Hofmann, Andreas , Preston, Sarah , Cross, Megan , Herath, Dilrukshi , Simon, Anne , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 20, no. (2019), p. 1-6
- Full Text:
- Reviewed:
- Description: Background: Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results: We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions: DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.
- Authors: Hofmann, Andreas , Preston, Sarah , Cross, Megan , Herath, Dilrukshi , Simon, Anne , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 20, no. (2019), p. 1-6
- Full Text:
- Reviewed:
- Description: Background: Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results: We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions: DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.
Phenotypic screening of the 'Kurz-box' of chemicals identifies two compounds (BLK127 and HBK4) with anthelmintic activity in vitro against parasitic larval stages of Haemonchus contortus
- Nguyen, Linh, Kurz, Thomas, Preston, Sarah, Brueckmann, Hjoerdis, Lungerich, Beate, Herath, Dilrukshi, Koehler, Anson, Wang, Tao, Skalova, Lenka, Jabbar, Abdul, Gasser, Robin
- Authors: Nguyen, Linh , Kurz, Thomas , Preston, Sarah , Brueckmann, Hjoerdis , Lungerich, Beate , Herath, Dilrukshi , Koehler, Anson , Wang, Tao , Skalova, Lenka , Jabbar, Abdul , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: Parasites & Vectors Vol. 12, no. (2019), p. 1-9
- Full Text:
- Reviewed:
- Description: BackgroundDue to anthelmintic resistance problems, there is a need to discover and develop new drugs for the treatment and control of economically important and pathogenic nematodes of livestock animals. With this focus in mind, we screened 236 compounds from a library (called the Kurz-box') representing chemically diverse classes such as heterocyclic compounds (e.g. thiazoles, pyrroles, quinolines, pyrimidines, benzo[1,4]diazepines), hydoxamic acid-based metalloenzyme inhibitors, peptidomimetics (bis- and tris-pyrimidoneamides, alkoxyamides) and various intermediates on Haemonchus contortus, one of the most important parasitic nematodes of ruminants.MethodsIn the present study, we tested these compounds, and measured the inhibition of larval motility and development of exsheathed third-stage (xL3) and fourth-stage (L4) larvae of H. contortus using an optimised, whole-organism phenotypic screening assay.ResultsOf the 236 compounds, we identified two active compounds (called BLK127 and HBK4) that induced marked phenotypic changes in the worm in vitro. Compound BLK127 induced an eviscerated' phenotype in the xL3 stage and also inhibited L4 development. Compound HBK4 exerted a curved' phenotype in both xL3s and L4s.ConclusionsThe findings from this study provide a basis for future work on the chemical optimisation of these compounds, on assessing the activity of optimised compounds on adult stages of H. contortus both in vitro and in vivo (in the host animal) and against other parasitic worms of veterinary and medical importance.
- Authors: Nguyen, Linh , Kurz, Thomas , Preston, Sarah , Brueckmann, Hjoerdis , Lungerich, Beate , Herath, Dilrukshi , Koehler, Anson , Wang, Tao , Skalova, Lenka , Jabbar, Abdul , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: Parasites & Vectors Vol. 12, no. (2019), p. 1-9
- Full Text:
- Reviewed:
- Description: BackgroundDue to anthelmintic resistance problems, there is a need to discover and develop new drugs for the treatment and control of economically important and pathogenic nematodes of livestock animals. With this focus in mind, we screened 236 compounds from a library (called the Kurz-box') representing chemically diverse classes such as heterocyclic compounds (e.g. thiazoles, pyrroles, quinolines, pyrimidines, benzo[1,4]diazepines), hydoxamic acid-based metalloenzyme inhibitors, peptidomimetics (bis- and tris-pyrimidoneamides, alkoxyamides) and various intermediates on Haemonchus contortus, one of the most important parasitic nematodes of ruminants.MethodsIn the present study, we tested these compounds, and measured the inhibition of larval motility and development of exsheathed third-stage (xL3) and fourth-stage (L4) larvae of H. contortus using an optimised, whole-organism phenotypic screening assay.ResultsOf the 236 compounds, we identified two active compounds (called BLK127 and HBK4) that induced marked phenotypic changes in the worm in vitro. Compound BLK127 induced an eviscerated' phenotype in the xL3 stage and also inhibited L4 development. Compound HBK4 exerted a curved' phenotype in both xL3s and L4s.ConclusionsThe findings from this study provide a basis for future work on the chemical optimisation of these compounds, on assessing the activity of optimised compounds on adult stages of H. contortus both in vitro and in vivo (in the host animal) and against other parasitic worms of veterinary and medical importance.
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