Moderator: Jean-Karim Heriche

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Posts by Jean-Karim Heriche

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Comment: C: Pagerank of Hippie genes
... The [wikipedia article on centrality][1] explains many centrality measures. However, you should ask yourself what kind of biological information you're trying to get at and in this context what node importance is (and whether it is relevant). Given that most biological networks are incomplete, many ...
written 2 days ago by Jean-Karim Heriche16k
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Comment: C: Pagerank of Hippie genes
... Given a square matrix A, λ and v are a number and vector respectively that satisfy the equation Av=λv. λ is called an eigenvalue and v is an eigenvector of A corresponding to the eigenvalue λ. You can see from the equation that multiplying v by a constant wouldn't change anything. This is basic lin ...
written 2 days ago by Jean-Karim Heriche16k
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Comment: A: Pagerank of Hippie genes
... By definition, you can scale an eigenvector and it will still be an eigenvector or put another way, the scale of an eigenvector is irrelevant. Many software will normalize eigenvectors to unit length. ...
written 2 days ago by Jean-Karim Heriche16k
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Answer: C: <3000$ in funding for computer equipment. Should I save this for cloud computing
... If your institution has a high performance computing cluster, then I would recommend to look into getting access to it or to one at a nearby institution. Regardless, you will always need some compute capacity in the lab so it's probably best to start with this. Cloud computing is good as a temporary ...
written 2 days ago by Jean-Karim Heriche16k
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Comment: C: ngs vs microarray
... I moved this to a forum post. ...
written 3 days ago by Jean-Karim Heriche16k
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Answer: A: ngs vs microarray
... There are probably many reasons. One may be the weight of inertia. If you know a technology and it works for you, there's little reason to switch to something else. For some applications, microarrays may be cheaper than NGS, especially if you factor in the cost of analysis because data handling and ...
written 3 days ago by Jean-Karim Heriche16k
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Comment: C: Math-CDF Perl Module compiler issue
... This is due to Apple having messed up with gcc in the past. See this [blog post][1]. Also, why would you use ActivePerl ? Mac OS comes already with perl installed and if you need another version, you should use [perlbrew][2]. By the way this is not a bioinformatics question. This should be posted on ...
written 3 days ago by Jean-Karim Heriche16k
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Comment: C: Resources for a systems biology approach to multiomics.
... It is usually a good idea to collect data with some idea of what one wants to get out of it. What kind of question can be addressed with your data depends on what the data represents and the context in which it was collected. How you approach your data analysis will depend on the question you want t ...
written 10 days ago by Jean-Karim Heriche16k
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Comment: C: Scale-free networks are rare
... Note that the generality of the scale-free notion and power law distribution of degrees have long been called into question, see for example [The powerful law of the power law and other myths in network biology][1] and [Power-law distributions in empirical data][2]. I'll have to read this paper but ...
written 10 days ago by Jean-Karim Heriche16k
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Answer: A: Hierarchical clustering evaluation
... The way to deal with large numbers of anything is to have a computer do the work. The question you should ask yourself is what are you trying to assess ? There are many ways to evaluate a clustering result but they depend on the context and the goal of the clustering. If you have anything resembling ...
written 10 days ago by Jean-Karim Heriche16k

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