http://brak.sdsc.edu/forum/discussions/feed.rss Wed, 16 May 12 18:01:55 -0400 All Discussions - BiologicalNetworks Forum en-u http://brak.sdsc.edu/forum/discussion/78/plotting-multiple-expression-matrices-onto-one-interaction-network Mon, 14 May 2012 13:57:01 -0400 Andrew Cowie 78@/forum/discussions
I have datasets of gene expression (microarray) and protein expression (quantitative by mass spec). I was wondering if Biological Networks is able to place both of these on the same network. ]]> http://brak.sdsc.edu/forum/discussion/77/building-pathways-from-list-of-sequences Sun, 15 Apr 2012 20:23:32 -0400 Amy 77@/forum/discussions
another feature I would like to see in BioNets is a function for creation Pathways/Networks starting form the list of sequences and their IDs. In a few of my recent experiments I've been working off of annotated sequences using one of the sequence analysis software, and finally
I have a list of sequences and Ensembl genes IDs. How can I find pathways these genes are involved in? Can I found regulators regulating transcription of these genes , common regulators?

Thank you for creating such a nice software!
]]> http://brak.sdsc.edu/forum/discussion/76/copypaste-network-with-atributes Sun, 15 Apr 2012 20:16:38 -0400 Amy 76@/forum/discussions
I am using BioNets for constructing networks from public databases. Being able
to construct big networks (using all shortest paths, direct/indirect targets functions) I frequently need to copy part of the big network, and then to paste into the empty new network.

How can I do that?
Also preferably that during the copy/paste all annotations, properties of nodes and interactions are saved not to rebuild/reannotate the network again.

Thank you.]]> http://brak.sdsc.edu/forum/discussion/75/i-have-a-list-of-genes Fri, 23 Mar 2012 14:36:21 -0400 zixing wang 75@/forum/discussions http://brak.sdsc.edu/forum/discussion/74/making-my-data-network-microarray-etc-public Wed, 29 Feb 2012 13:49:43 -0500 cc Dana 74@/forum/discussions ]]> http://brak.sdsc.edu/forum/discussion/73/weighting-interaction-edges Wed, 22 Feb 2012 22:52:14 -0500 Sebastian 73@/forum/discussions
where can I find methods used for the representation of edges/relations in BiologicalNetworks? In other words how do you weight co-citation edges mentioning two genes or proteins in one Abstract/Sentence?
Also how do you integrate edges having different types of evidence, for example co-citation with protein-protein interaction and co-expression between the same two genes/proteins?
And the last, how do you derive causal/directional edges, do you do NLP of PubMed abstracts?

Thanks.

And Thank you for this piece of software, Good job!
]]> http://brak.sdsc.edu/forum/discussion/71/merging-network-pathways Fri, 20 Jan 2012 04:09:41 -0500 Wang 71@/forum/discussions
I am new to BiologicalNetworks and am currently using it to view gene interaction networks and pathways. I am wondering how i could build interaction networks for say NF-kB and EGFR at the same time and then how i could merge these two networks?

Also, is there a way to display these interactions with other proteins in a certain
pathway for example from KEGG or Reactome?

Thanks!

]]> http://brak.sdsc.edu/forum/discussion/70/interaction-networks Mon, 28 Nov 2011 14:00:44 -0500 Dave 70@/forum/discussions
I need to construct an interaction network, for my list of genes coming from screening experiment. My organism is mouse. I tried to import my list of genes into the system, but not sure I am doing this in a right way. I also would like to visualize my expression data on the network: I'd like the color of the node related to expression and/or thickness of the edge related to the strength of co-expression.
How can I do that in your system?

Thanks.

]]> http://brak.sdsc.edu/forum/discussion/48/e-mail-notification-of-new-posts-on-the-forum Thu, 31 Mar 2011 02:42:38 -0400 BN_ 48@/forum/discussions
We have a number of inquiries from our users such as: "It would be great to have an option for email notification when someone's responds to my post".

Now, when someones responds to your post you will get a notification to your email address.

Thanks.
]]> http://brak.sdsc.edu/forum/discussion/68/co-expressed-genes-from-geo Sat, 29 Oct 2011 22:04:10 -0400 Anand 68@/forum/discussions
I was trying to run a search for genes co-expressed with my list of genes from GEO using your
MicroarrayPanel. So I load my list of genes and specified organism "Mouse", bu the search results didnt come out. Are there any other parameters I have to specify for multi-experiment microarray search?

Thank you for doing a great job!
]]> http://brak.sdsc.edu/forum/discussion/66/how-to-load-gene-and-relation-properties Mon, 03 Oct 2011 22:57:09 -0400 Jeff Backer 66@/forum/discussions
how can I load my network with my properties for genes and proteins and their relations together with attributes that are shown from your database?

Thanks!

]]> http://brak.sdsc.edu/forum/discussion/65/how-to-get-pathways-or-genomes-genes-from-kegg-map Mon, 26 Sep 2011 19:06:00 -0400 paokmaniak 65@/forum/discussions Thank you]]> http://brak.sdsc.edu/forum/discussion/64/how-to-construct-a-network-with-subnetwork Tue, 30 Aug 2011 18:01:18 -0400 Matt 64@/forum/discussions
I have a transcription factor gene interaction network. And genes are grouped into subgroups/subnetworks. How can I create such a network? I have a .sif file for TF-gene network, and I have files, groups in an Excell table (every column a group).

Thanks in advance!
]]> http://brak.sdsc.edu/forum/discussion/63/homologous-network-construction Sat, 30 Jul 2011 07:21:54 -0400 Andrew 63@/forum/discussions
thank you very much for such a nice piece of software. Great job!

I have a question about construction of homologous networks. May be I missed someth,
but I couldn't find in your tutorials how I can construct a homologous network (let's say mouse)
from a given one (for example Human). We are studying conservation of different molecular modules like protein complexes starting from lower organisms such as Drosophila up to Humans.

Thanks in advance for you help! ]]> http://brak.sdsc.edu/forum/discussion/62/saving-as-sbml-file Wed, 06 Jul 2011 14:57:57 -0400 Mike 62@/forum/discussions
how can i save my network as SBML file to use it in further analysis?

Thanks!]]> http://brak.sdsc.edu/forum/discussion/60/how-to-increase-memory-settings Mon, 20 Jun 2011 21:16:43 -0400 Mark 60@/forum/discussions
I am using a 2.5 Ghz, 4Gb Ram, windows Vista laptop.
What are the default settings for memory usage for the program? because it looks like it becomes a little bit sluggish on big network visualizations and microarray files.
How can I increase default memory settings?

Thanks.
Mark.
]]> http://brak.sdsc.edu/forum/discussion/59/how-to-change-node-shapes Wed, 01 Jun 2011 23:26:17 -0400 Mike 59@/forum/discussions
I have a question on changing node shapes. I have a file with interaction pairs:

Small_Molecule1 Protein1
Small_Molecule2 Protein2
etc


How can I specify different shapes to different object types?


Thanks.
]]> http://brak.sdsc.edu/forum/discussion/56/color-nodes-by-multiple-colors-multiple-parameter-values Mon, 23 May 2011 22:08:18 -0400 Gregor 56@/forum/discussions
I need to color my nodes by cellular localization (e.g. GeneOntology Cellular_Component parameter). Since some of the proteins have simultaneously several localizations (e.g. move from cytoplasm to nucleus and back) is there a way in BioloigcalNetworks to give two (eg half node each) or more colors to a node? This should be based on two or more attributes.

For example:

-red nodes- Nucleus
-green nodes- Cytoplasm
-half red half green- both Nucleus and Cytoplasm

based on the fact what the GeneOntology Cellular_Component value is.


Thanks!
Gregor
]]> http://brak.sdsc.edu/forum/discussion/57/systems-biology-conference-folow-up Mon, 23 May 2011 22:51:39 -0400 Tim 57@/forum/discussions
First of all let me thank you for our nice discussion during the Sys Bio Conference last Friday at SALK. It was great poster session and great discussion!
It was nice to meet you and get this started; and I'm looking forward to what I hope will be a really exciting project.

I'm writing to let you know that I'll try to make the necessary tweaks to my code ASAP in order to give you a list of targets and sequence data that fits what we discussed, by which time I'll be sending you everything I promised (the data, the presentation, etc).

Thanks again, and I'll be in touch again shortly!
Tim.
]]> http://brak.sdsc.edu/forum/discussion/55/custom-layouts Mon, 16 May 2011 03:25:48 -0400 Robert 55@/forum/discussions
I've been playing with BN for a few days with a goal of trying different layout options on the networks produced from searching your database.

I've noticed a nice feature of meta-nodes layouting, but could not find just layouting of selected nodes (without creating a meta-node with selected nodes). Can I layout just selected nodes?

Also when doing a meta-node sublayout I cannot scale (Can I?) the subnetwork, without scaling the meta-node, and most central nodes are layed upon each other.

Also I need to layout nodes of certain types, let's say Transcription Factors and make them aligned hierarchically, but the position should remained "almost" the same. Is this possible to do in BiologicalNetworks? If yes, how... I noticed I can select by type (TF), I can do hierarchical layout, but i could' t figure out how to use this together.

Thanks a lot!
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