Comments for Steve's Systems Biology blog

Comment on XPPAUT by Gesilda Florenço

Gesilda Florenço — Fri, 03 Feb 2012 13:42:41 +0000

Hello! thanks for the answer! I’m sending the model below the article by Bertram (2000).

# Phantom bursting model, with 2 fast and 2 slow variables.
# Bertram et al, Biophys. J. 79:2880-2892, 2001.
# For Fig. 2, set gs1=20.
# For Fig. 3, set gs1=7, set v(0)=0.6, set total integration time = 120000.
# For Fig. 4, set gs1=3, set v(0)=0.6, set total integration time = 300000.

# Units: V = mV; t = ms; g = pS; I = fA

# Initial conditions
v(0)=-43
n(0)=0.03
s1(0)=0.1
s2(0)=0.434

# Parameters

param lambda=1.1, gca=280, gk=1300
param gl=25, vs1=-40, taus1=1000, vs2=-42, taus2=120000, gs2=32
param gs1=7, vl=-40

param vca=100, vk=-80, cm=4524
param tnbar=9.09, vm=-22, vn=-9, sm=7.5, sn=10

param ss1=0.5, ss2=0.4

# activation and time-constant functions
minf(v) = 1.0/(1.0+exp((vm-v)/sm))
ninf(v) = 1.0/(1.0+exp((vn-v)/sn))
taun(v) = tnbar/(1.0+exp((v-vn)/sn))
s1inf(v) = 1.0/(1.0+exp((vs1-v)/ss1))
s2inf(v) = 1.0/(1.0+exp((vs2-v)/ss2))

# ionic currents
ica(v) = gca*minf(v)*(v-vca)
ik(v) = gk*n*(v-vk)
il(v) = gl*(v-vl)
is1(v) = gs1*s1*(v-vk)
is2(v) = gs2*s2*(v-vk)

# differential equations
v’ = -( ica(v) + ik(v) + il(v) + is1(v) + is2(v) )/cm
n’ = lambda*(ninf(v) – n)/taun(v)
s1′ = (s1inf(v) – s1)/taus1
s2′ = (s2inf(v) – s2)/taus2

# XPP parameters
@ meth=cvode, dtmax=1, dt=5, total=120000, maxstor=100000
@ bounds=100000000, xp=t, yp=v, toler=1.0e-6, atoler=1.0e-6
@ xlo=0, xhi=30000, ylo=-70, yhi=-10

done

Comment on XPPAUT by Steve

Steve — Wed, 01 Feb 2012 17:38:11 +0000

sure, if you send your model over and what you want to plot I can take a quick look at it. Also, if you’re going to be working with XPPAUT a lot, there’s the accompanying text book: “simulating, analyzing, and animating dynamical systems” which is really good.

Comment on XPPAUT by Gesilda Florenço

Gesilda Florenço — Wed, 01 Feb 2012 17:23:27 +0000

Hello! I found an article in xppaut, I liked the program but I need a phasespace do not know how to do, I’ve tried various ways, but nothing appears!

Can anyone help me?!
I’m wanting the phasespace model Bertram (2000) in xppaut.
gesildaflorenco@gmail.com

Comment on Python and Systems Biology by Shaxie

Shaxie — Wed, 14 Dec 2011 07:25:34 +0000

Thanks for pointing out systems biology packages in Python.

Comment on XPPPad by Bard

Bard — Sat, 10 Dec 2011 02:53:13 +0000

Yup. No auto. Sorry but we felt it would be too hard. Also auto does a ton of disk seeking and is really easy to crash. One writer noted that ode solvers are 2 a penny. But in fact, there seem to be no ode solvers on the iPad except XPP and a recent one that is pretty lame. XPP has some aspects that are not on the desktop version such as the ability to watch invariant manifolds move around as you change parameters. It has all the other capabilities such as stability, animations, PDEs delay equations, boundary value problems etc. you can do some orbit diagrams eitc which are not quite bifurcation diagrams.

Comment on 11th hour by Steve

Steve — Fri, 28 Oct 2011 09:28:33 +0000

Hi, thanks for visiting my blog My experience was shared by a number of others on our DTC unfortunately. Hopefully yours will be better organised and managed. Make sure you keep an eye on 2 things during your Ph.D: 1) Publication; see if you can produce a mini-review from your literature review, and structure your work throughout towards at least one publication. Writing a publication will help enormously towards writing your thesis, as well as your career; writing is a skill as much as doing a western blot, or coding. 2) Keep in mind what kind of job you want at the end, and make sure you develop skills in those areas so that you are employable at the end. I would recommend focusing on either wet skills or dry skills, and just give a passing nod to the minor one to keep the DTC happy (we had to do a combination wet and dry and I got the balance just off to be employed at either). Research and industry projects do not employ people who are good at both, they look for specialist experts and form multi-skilled teams. This is something to consider when you’re skilling up in your Ph.D.

At the moment, I’ve applied for a couple of post-doc positions, but the “systems biology” roles are all looking for mathematicians or statisticians, and bioengineering isn’t happening in the UK. For systems biology. there are no posts requiring skills in life sciences, other than generally knowing they exist. They want mathematicians to build models from data obtained from collaborating wet labs. I’m currently re-skilling in PHP and Python programming while awaiting a viva date, and if I’m fortunate enough to get through, I’ll be looking at freelance web design, or coding jobs so I don’t have to return to factory QC microbiology (my B.Sc training). Our DTC really let the wet lab scientists down in terms of skills and career development, and none of us have jobs at the moment. We’re all frantically re-skilling, after spending 4 years re-skilling. It’s quite frustrating. I would probably recommend sticking to programming, and as much computational work as you can, as the dry scientists are doing pretty well with well paid posts in bioinformatics and modeling. Stochastic simulations and the accompanying statistics are quite popular at the moment too, and worth adding to your CV.

Also remember that conferences are massively important to attend. Focus on networking while you’re there. It’s not about the science, it’s about the contacts you make for post doc positions when you finish. Sell yourself and your science and don’t be a wall flower

That’s my 10p of advice anyway )) Hope it does go well, I still believe systems biology is a valuable field for the future.

Comment on 11th hour by Michael

Michael — Thu, 27 Oct 2011 21:41:00 +0000

A pitty your PhD ended up such a bad experience for you. I just started my own sysbio PhD at a DTC, hope it will go differently.. I enjoyed reading your blog, hope you still keep posting. Where are you going to from academia?

Comment on all stop by Steve

Steve — Wed, 05 Oct 2011 20:42:05 +0000

it’s a broad topic. you would have to provide some more specific details.

Comment on all stop by sanhita ray

sanhita ray — Wed, 05 Oct 2011 19:48:35 +0000

bst of luck!! ..i am a recent graduate..can u tellme sm gud resources on the basics of noise??

Comment on Ph.D? Ph. don’t. by mne

mne — Tue, 13 Sep 2011 13:44:22 +0000

yeah, the situation is pretty bleak, but you shouldn’t think that this is unique to the field of science.
there is an oversupply of graduates in business, economics, law, not to speak of the humanitites. they all have their nightmare stories. the funding situation can be much worse there too, and there is no industry to speak of.
so i guess what you describe is symptomatic to how our society works in general and not (just) of science.