What is best tool for boolean modelling with limited experimental data?

More Ashmit Singh's questions See All

How to add an outgroup while using supermatrix approach for species tree reconstruction?

I have 12 species from same genus. For supermatrix approach we generally use the multiple sequence alignment single copy orthologs sequences then concatenate them and remove the badly aligned...

11 December 2017 3,868 4 View

What is the difference between analysis of recombination and selection pressure when using multiple Genus vs multiple species?

I read several papers where researchers use several strains of same species for analysis of recombination or selection pressure however there are few papers in which researchers use the multiple...

09 October 2017 8,848 4 View

Do I need to stick with single copy orthologs, while estimating selection pressure with PAML?

The ortholog groups of 5 species proteins look like: Group1: sp1 sp2 sp3 sp4 sp5 Group2: sp1 sp2_seq1 sp2_seq2 sp3 sp4_seq1 sp4_seq2 sp5 (sp is for species here) As here one can see the Group1...

05 June 2017 6,710 1 View

How can I evaluate the accuracy of predicted protein protein interactions with ROCR package?

I need to evaluate the accuracy of predicted interactome of an insect species which I constructed by interolog method. I read that I can use ROCR package for it. I got a gold standard positive PPI...

02 March 2017 9,554 1 View

Which type of Tree is needed for codeml PAML analysis?

I need to run codeml for ortholog clusters from different related genus. Do I need to generate a species tree for it that I can use for all the clusters or I need to generate gene tree for all the...

01 February 2017 2,304 3 View

How to identify irreversible reactions and inconsistency of KEGG reactions?

Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG

06 July 2016 4,805 3 View

Which journals you regularly follow to increase your knowledge-base?

In principle, this questions is like quora flavor. Here, I am asking this question for a bioinformatician perspective but surely would like to know you opinion about the other journals that are...

04 May 2016 7,593 2 View

How the large scale signaling network can be converted into Boolean model?

PS: I have single time point gene expression data for around half of the gene in the signaling network.

04 May 2016 3,055 2 View

How can I apply z-test for significance changes in the protein-protein interaction network properties while comparing with random networks?

I have created a PPI network, now I want to compare it with random networks. I can generate the random network. In general, I am interested in the comparision plots of (i) degree vs betweenness...

03 April 2016 10,079 4 View

What is the biological significance of under-representation of differentially expressed genes?

I understand the over-representation of GO term in FDR test against reference gene sets but the under-representation seems confusing. My test set is infection induced differentially expressed...

03 April 2016 3,359 5 View

Could you recommend some articles on Urban Transportation System optimization and Innovation?

13 August 2024 2,595 3 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Kushal Suryamohan

You can try using this tool - GeNE Tool (from Eric Davidson's lab) - see attached files. Still in beta testing mode, I think, but it works fine (does tend to hang up abruptly, so my advice - save frequently).

Lori Clow

Curious as to why you want to use Boolean modelling? Typically for describing only two states. Of course, I do not know what exactly you are attempting to achieve. Have you looked at REVEAL (Liang et al.)? Good luck!

Ashmit Singh

@Lori - The objective here is to simulate the pathway with some unreported ligands to define their role in infection. I will also have a look on Reveal.