January 2022 Commit Log

Number of Commits:
232
Number of Active Developers:
2
sbu062 2022-01-31 18:24 Rev.: 12125

need sergey also in list

1 lines of code changed in 1 file:

sbu062 2022-01-31 18:22 Rev.: 12124

mailing list to top

9 lines of code changed in 1 file:

sbu062 2022-01-31 18:20 Rev.: 12123

added mailing list

10 lines of code changed in 1 file:

sbu062 2022-01-29 18:04 Rev.: 12122

resubmit r12121

1256 lines of code changed in 1 file:

sbu062 2022-01-29 17:59 Rev.: 12121

small fix

1 lines of code changed in 1 file:

sbu062 2022-01-29 14:16 Rev.: 12120

resubmit after webform addition r12119

1364 lines of code changed in 1 file:

sbu062 2022-01-29 14:13 Rev.: 12119

fix wording

1 lines of code changed in 1 file:

sbu062 2022-01-29 14:12 Rev.: 12118

add note on team in webform project summary

2 lines of code changed in 1 file:

sbu062 2022-01-29 14:05 Rev.: 12117

resubmit r12116

2196 lines of code changed in 1 file:

sbu062 2022-01-29 14:02 Rev.: 12116

add `Revision` keyword to file properties

6082 lines of code changed in 1 file:

sbu062 2022-01-29 14:00 Rev.: 12115

remove `Revision` tag at footer

6982 lines of code changed in 1 file:

sbu062 2022-01-29 13:59 Rev.: 12114

reference list: add indents for numbers for easier reading, fit 11 pages

6301 lines of code changed in 1 file:

sbu062 2022-01-29 13:50 Rev.: 12113

resubmit r12112

7533 lines of code changed in 1 file:

sbu062 2022-01-29 13:44 Rev.: 12112

minor text adjust

6252 lines of code changed in 1 file:

sbu062 2022-01-29 13:43 Rev.: 12111

small adjustment of some figures

6084 lines of code changed in 1 file:

sbu062 2022-01-29 13:40 Rev.: 12110

firgotten highlight deleted

6196 lines of code changed in 1 file:

sbu062 2022-01-29 13:39 Rev.: 12109

manually edited list of references, highlight team members refs etc

6896 lines of code changed in 1 file:

sbu062 2022-01-29 12:58 Rev.: 12108

added reference to Rønnestad & Budaev digital twin model as 49, need reformatting reference list

6551 lines of code changed in 1 file:

sbu062 2022-01-29 12:33 Rev.: 12107

small fixes to fit 11 pages

6367 lines of code changed in 1 file:

sbu062 2022-01-29 12:23 Rev.: 12106

fix figure 6 to avoid extra space below

6263 lines of code changed in 1 file:

sbu062 2022-01-29 12:21 Rev.: 12105

added Marco and fixed partner participation in WPs

6966 lines of code changed in 1 file:

sbu062 2022-01-29 12:16 Rev.: 12104

goes to numbered files

0 lines of code changed in 2 files:

sbu062 2022-01-29 12:14 Rev.: 12103

added Marco's CV
> From: Marco Del Giudice <marcodg@unm.edu>
> To: Sergey Budaev <sergey.budaev@uib.no>
> Subject: Re: Norwegian Research Council project: STRESSALGO: an invitation
> Date: Fri, 28 Jan 2022 15:57:28 -0700
>
> Here you go. Let me know if it works.
>
> Cheers,
>
> M

0 lines of code changed in 1 file:

sbu062 2022-01-28 16:00 Rev.: 12102

resubmit r12101

1594 lines of code changed in 1 file:

sbu062 2022-01-28 15:57 Rev.: 12101

new fig.2 svg as r12100

5744 lines of code changed in 1 file:

sbu062 2022-01-28 15:56 Rev.: 12100

forgotten svg for fig. 2

6 lines of code changed in 1 file:

sbu062 2022-01-28 15:54 Rev.: 12099

resubmit with adjusted fig.2 as r12097

1657 lines of code changed in 1 file:

sbu062 2022-01-28 15:49 Rev.: 12098

adjusted fig. 2: separate stimuli pools, left and right panels closer
> I suggest a change in fig 2. On top there seems to be "something" that feeds into 3 SCs which integrate and make a GOS.
> 1) it would be better to have a grey "explosion" above each SC, ao the reader does not think this is a single event.
> 2) The arrow from stimulus to response should have been broken with explanatory texts: "Competition between SCs" and "strongest SC taking control"

577 lines of code changed in 2 files:

sbu062 2022-01-28 11:28 Rev.: 12097

minor, wording

5645 lines of code changed in 1 file:

sbu062 2022-01-28 11:23 Rev.: 12096

resubmit for r12095

1848 lines of code changed in 1 file:

sbu062 2022-01-28 11:05 Rev.: 12095

a few fixes

5699 lines of code changed in 1 file:

sbu062 2022-01-28 01:11 Rev.: 12094

new resubmission after Barbara have joined

8359 lines of code changed in 1 file:

sbu062 2022-01-28 01:04 Rev.: 12093

Barbara Taborsky is also in project

41 lines of code changed in 1 file:

sbu062 2022-01-28 01:03 Rev.: 12092

now include Barbara Taborsky in the project

6463 lines of code changed in 1 file:

sbu062 2022-01-28 00:48 Rev.: 12091

numbered

0 lines of code changed in 2 files:

sbu062 2022-01-28 00:47 Rev.: 12090

pdf of BT CV produced in Word

0 lines of code changed in 1 file:

sbu062 2022-01-28 00:44 Rev.: 12089

added CV of Barbara Taborsky
> From: <barbara.taborsky@iee.unibe.ch>
> To: <sergey.budaev@uib.no>
> Subject: RE: Norwegian Research Council project: STRESSALGO: an invitation
> Date: Fri, 28 Jan 2022 00:23:32 +0000
>
> Hi Sergey,
>
> Sure, it would be an honour to be involved in this interesting project.
>
> Thanks for the text (the grant now has a new number, but still the same grant.
> I did not see the CV template attached, maybe you forgot?
> But I am afraid, as I am leaving tomorrow and its late, I can anyway not do much on it. I send you a CV, which by conincidence has 4 ages, but it’s the format I needed for the Swiss funding agency where I applied in autumn
> I also send a more or less actualized publication list of the past 5 years I had prepared for that. it has two pages.
>
> So if the 2 pages "major achievements" in the CV are not suitable, you could replace them by the 2 pages ref list.
>
> As I did not get the template I don't know what is best, but perhaps the CV is allright as it is.
>
> Again, good luck and please let me know how everythign worked out
> Barbara

0 lines of code changed in 1 file:

sbu062 2022-01-28 00:27 Rev.: 12088

submitted r12087

1481 lines of code changed in 1 file:

sbu062 2022-01-28 00:23 Rev.: 12087

need highlight more refs as belonging to the team

6467 lines of code changed in 3 files:

sbu062 2022-01-28 00:07 Rev.: 12086

submitted project after Lynne's changes

26742 lines of code changed in 1 file:

sbu062 2022-01-28 00:01 Rev.: 12085

merged Lynne's changes
> From: Lynne Sneddon <lynne.sneddon@bioenv.gu.se>
> To: Sergey Budaev <sergey.budaev@uib.no>, Jarl Giske <Jarl.Giske@uib.no>
> CC: "Kristiansen, Tore" <torek@hi.no>, Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: Re: STRESSALGO r12058
> Date: Thu, 27 Jan 2022 22:23:07 +0000
>
> Dear Sergey,
>
> I put my comments and edits on the last version Jarl sent. It's a fascinating proposal.
>
> Best wishes,
> Lynne

4649 lines of code changed in 1 file:

sbu062 2022-01-27 23:15 Rev.: 12084

primary objective from main text after JG edition

1 lines of code changed in 1 file:

sbu062 2022-01-27 23:10 Rev.: 12083

remove svn tags from CV

0 lines of code changed in 1 file:

sbu062 2022-01-27 23:07 Rev.: 12082

need numbered CV files for easier attaching and management

3244 lines of code changed in 13 files:

sbu062 2022-01-27 23:02 Rev.: 12081

HZ's CV in pdf

15 lines of code changed in 2 files:

sbu062 2022-01-27 22:57 Rev.: 12080

lowest order red subtitles all italic, red color not brick

5809 lines of code changed in 1 file:

sbu062 2022-01-27 22:53 Rev.: 12079

color red not brick

5812 lines of code changed in 1 file:

sbu062 2022-01-27 22:50 Rev.: 12078

there is space to put Tores name

6097 lines of code changed in 1 file:

sbu062 2022-01-27 22:49 Rev.: 12077

need Tores name

119 lines of code changed in 1 file:

sbu062 2022-01-27 22:45 Rev.: 12076

second part of Jarl's comments and changes
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> CC: "Kristiansen, Tore" <torek@hi.no>
> Subject: RE: STRESSALGO r12058
> Date: Thu, 27 Jan 2022 20:15:58 +0000
>
> Here are comments to pages 3-6.
> The comments I sent earlier today to pages 1-2 are not in this document.
> Jarl

1817 lines of code changed in 1 file:

sbu062 2022-01-27 22:42 Rev.: 12075

highlight team member publications as in main document

129 lines of code changed in 1 file:

sbu062 2022-01-27 20:29 Rev.: 12074

did first portion of Jarl's comments, references need red-highlighting manually redone
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>, "Kristiansen, Tore" <torek@hi.no>
> CC: Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, Lynne Sneddon <lynne.sneddon@bioenv.gu.se>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: RE: STRESSALGO r12058
> Date: Thu, 27 Jan 2022 12:49:50 +0000
>
> Very nice, Sergey! To see it all in 11 pages.
> Here are some suggestions from me to increase readability of the 2 first pages.
> Can you see comments in the margin? Or shall I convert to a different format for comments?
> jarl

6306 lines of code changed in 1 file:

sbu062 2022-01-27 20:25 Rev.: 12073

set books bold for easy re-editing main document

55 lines of code changed in 1 file:

sbu062 2022-01-27 19:24 Rev.: 12072

put date of birth for Hector's CV
> From: Hector Zenil <hzenilc@gmail.com>
> To: Sergey Budaev <sergey.budaev@uib.no>
> Subject: Re: Norwegian project: STRESSALGO
> Date: Thu, 27 Jan 2022 22:47:49 +0400
>
> Great. Very interesting project, I wish I had more time to give you
> feedback on short notice.
>
> DOB 26/02/1977
>

13 lines of code changed in 1 file:

sbu062 2022-01-27 17:43 Rev.: 12071

some typos fixed

235 lines of code changed in 1 file:

sbu062 2022-01-27 17:16 Rev.: 12070

quickly compiled HZ's CV from long CV_HZ_Oxford.pdf

1840 lines of code changed in 1 file:

sbu062 2022-01-27 15:39 Rev.: 12069

added pdf generated from fodt

0 lines of code changed in 1 file:

sbu062 2022-01-27 15:38 Rev.: 12068

maximum 10 relevant publications allowed, added software repos

0 lines of code changed in 1 file:

sbu062 2022-01-27 15:23 Rev.: 12067

add incoming CVs

0 lines of code changed in 3 files:

sbu062 2022-01-27 15:22 Rev.: 12066

fix role
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: RE: STRESSALGO r12058
> Date: Thu, 27 Jan 2022 14:55:00 +0000
>
> -----Original Message-----
> From: Sergey Budaev <sergey.budaev@uib.no>
> Sent: Thursday, January 27, 2022 3:02 PM
> To: Jarl Giske <Jarl.Giske@uib.no>
> Subject: Re: STRESSALGO r12058
>
> Just found a small issue, your CV has tick on Project manager
>
> S

0 lines of code changed in 1 file:

sbu062 2022-01-27 15:03 Rev.: 12065

refreshed and adapted CV for STRESSALGO

0 lines of code changed in 1 file:

sbu062 2022-01-27 12:16 Rev.: 12064

more refs highlighted red as team members

5645 lines of code changed in 1 file:

sbu062 2022-01-27 12:03 Rev.: 12063

move temporary (frozen) docs for highlighting and checking refs to etc

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sbu062 2022-01-27 11:59 Rev.: 12062

copied earlier master doc for special versions to check references and select team members' refs (red bold in final document)

0 lines of code changed in 2 files:

sbu062 2022-01-27 11:41 Rev.: 12061

jensen must be highlighted

5971 lines of code changed in 1 file:

sbu062 2022-01-27 11:33 Rev.: 12060

manually increase size of gnall chart breaking align lines, this makes figure better fit on white space

291 lines of code changed in 2 files:

sbu062 2022-01-27 11:25 Rev.: 12059

fix red fighlight in ref list

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sbu062 2022-01-27 11:13 Rev.: 12058

manual editing books in ref list: books need full titles

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sbu062 2022-01-27 10:53 Rev.: 12057

style for figure legends dark blue

5717 lines of code changed in 1 file:

sbu062 2022-01-27 10:46 Rev.: 12056

publications by team members highlighted red bold

5890 lines of code changed in 1 file:

sbu062 2022-01-27 10:43 Rev.: 12055

small adjustments

5656 lines of code changed in 1 file:

sbu062 2022-01-27 10:41 Rev.: 12054

fix typos

6355 lines of code changed in 1 file:

sbu062 2022-01-27 10:40 Rev.: 12053

small adjustments, figures, borders, fig 1 not full width any more

5963 lines of code changed in 1 file:

sbu062 2022-01-27 10:24 Rev.: 12052

select and highlight publications by team members red

5667 lines of code changed in 1 file:

sbu062 2022-01-27 10:10 Rev.: 12051

adjust position of figs, figure numbered manually because Fig 3 was 6

2161 lines of code changed in 1 file:

sbu062 2022-01-27 10:01 Rev.: 12050

fix introduction as suggested by Jarl after Tore
> From: "Kristiansen, Tore" <torek@hi.no>
> To: Sergey Budaev <sergey.budaev@uib.no>
> CC: Jarl Giske <Jarl.Giske@uib.no>, Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, "Lynne Sneddon" <lynne.sneddon@bioenv.gu.se>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: RE: STRESSALGO webforms updated
> Date: Thu, 27 Jan 2022 09:00:31 +0000
>
> Hi Sergey, all
>
> I also think the main focus should be on modelling and understanding stress, but since (we believe?) stress is caused by uncertainties (uncertain beliefs) and prediction errors (surprises, unpredicted changes) about the near future, and/or deviations between current state and the animals goal state (too hot, too exposed, too little food, etc.), I think this (uncertainties) must be central for modelling and testing of models and design of experiments, and understanding stress. The stress response is mainly mobilization of energy and attention to handle near future challenges. Stress is also a bit over used and much studied concept, so we need to find a way to give the evaluators a feeling of new and exciting discoveries.
>
> Cheers
> Tore
--------------------------------------------
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> CC: "Kristiansen, Tore" <torek@hi.no>
> Subject: RE: STRESSALGO r12029
> Date: Thu, 27 Jan 2022 09:19:49 +0000
>
> "To survive and thrive, animals need efficient strategies to reduce uncertainties about their environment and the results of their actions. They have evolved adaptive behavioural strategies for this."
>
> I do not like these sentences, for many reasons.
> 1) to include "thrive" can give the reader the impression that we think that evolutionary processes are work to make life good for animals.
> 2) To say "they have evolved" is to place the animal as actors in their evolution, as if they themselves have orchestrated the process (in order to thrive).
> 3) They are not only uncertain about the results of their actions, but also the results of the options they did not take.
>
> This is why I suggested this change to Tore's text:
> "To survive and reproduce, a mobile animal benefits from efficient strategies to reduce uncertainties about the state of its environment and the effects of its behavioural options. Adaptive strategies for dealing with uncertainty have therefore emerged during evolution."
>
> To keep it in line with Sergey's new text, I suggest
> "To survive and reproduce, animals benefit from efficient strategies to reduce uncertainties about their environment and the results of their actions. Adaptive strategies for this have therefore emerged during evolution."
> Or, ever better, I think (and then rewritten to singular form):
> "To survive and reproduce, an animal benefits from efficient strategies to reduce uncertainties about the state of its environment and the potential effects of its behavioural options. Adaptive strategies for this have therefore emerged during evolution."

5654 lines of code changed in 1 file:

sbu062 2022-01-27 09:58 Rev.: 12049

border for SC GOS label

5683 lines of code changed in 1 file:

sbu062 2022-01-27 09:52 Rev.: 12048

frame label with SC and GOS

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sbu062 2022-01-27 09:22 Rev.: 12047

SC and GOS capitalized to improve noticeability

6196 lines of code changed in 1 file:

sbu062 2022-01-27 07:51 Rev.: 12046

reference list: manual edit paragraph style to compact

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sbu062 2022-01-27 07:49 Rev.: 12045

fixed typo with refs, no manual editing so far

5745 lines of code changed in 1 file:

sbu062 2022-01-27 07:34 Rev.: 12044

fixing refs with explicit authors e.g. Zavala (2000)

5773 lines of code changed in 1 file:

sbu062 2022-01-27 02:12 Rev.: 12043

Feynman in red

5888 lines of code changed in 1 file:

sbu062 2022-01-27 02:11 Rev.: 12042

title line needs small lower spacing

5642 lines of code changed in 1 file:

sbu062 2022-01-27 02:10 Rev.: 12041

figure legend style no left indent

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sbu062 2022-01-27 01:57 Rev.: 12040

add footer with page number, page size lower border adjusted

6654 lines of code changed in 1 file:

sbu062 2022-01-27 01:38 Rev.: 12039

adjust and fix references as footnotes

6366 lines of code changed in 1 file:

sbu062 2022-01-27 01:33 Rev.: 12038

first paragraph no indent, adjust list of references paragraph, no ident

5523 lines of code changed in 1 file:

sbu062 2022-01-27 01:22 Rev.: 12037

global style adjust: mostly zero spaces before and after paragraphs

4643 lines of code changed in 1 file:

sbu062 2022-01-27 01:13 Rev.: 12036

anchor figs to page, except Fig. 4 and Gnatt

32715 lines of code changed in 1 file:

sbu062 2022-01-27 01:03 Rev.: 12035

use minimal reference style with three-column final list: nearly fitting

5650 lines of code changed in 1 file:

sbu062 2022-01-27 00:54 Rev.: 12034

reduced spacing after default paragraph style

1784 lines of code changed in 1 file:

sbu062 2022-01-27 00:51 Rev.: 12033

abridged references, round 1

48 lines of code changed in 1 file:

sbu062 2022-01-26 23:52 Rev.: 12032

reference style Evol. Ecol

167 lines of code changed in 1 file:

sbu062 2022-01-26 23:35 Rev.: 12031

try reference style Aquaculture

4983 lines of code changed in 1 file:

sbu062 2022-01-26 23:13 Rev.: 12030

typo fixed: random inserted text presumably from ref

5082 lines of code changed in 1 file:

sbu062 2022-01-26 19:41 Rev.: 12029

adjust fig position, with floating anchoring

4856 lines of code changed in 1 file:

sbu062 2022-01-26 19:37 Rev.: 12028

adjust position of floating figs, need anchoring to page

4833 lines of code changed in 1 file:

sbu062 2022-01-26 19:32 Rev.: 12027

corrections based on Tore Kristiansen
> From: "Kristiansen, Tore" <torek@hi.no>
> To: Sergey Budaev <sergey.budaev@uib.no>, Jarl Giske <Jarl.Giske@uib.no>
> CC: Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, Lynne Sneddon <lynne.sneddon@bioenv.gu.se>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: RE: STRESSALGO webforms updated
> Date: Wed, 26 Jan 2022 15:54:21 +0000
>
> Hi Sergey and Jarl,
>
> Attached are some comments and suggestions. The text still need to more structured and simplified and clear if we shall convince the evaluators, and catch their attention and get them excited about the project, (but I guess this is something you are well aware of). At the moment too many words and references, and a bit too complicated to follow. I suggest we also put a stronger focus on the relationship between uncertainty and stress, and the uncertainty about the brains perception and predictions (that can be leading to stress and anxiety, ..), and how and what strategies are best under uncertain conditions. This will depend on the development stage and environment (e.g. if it can starve for hours or weeks, etc,). All organisms (except cats) can only die once, so risk avoidance should be preferred? (The Darwinians are however more concerned about the opportunities for sex and this is correlated with some stupid and risk taking behaviours, especially by males : ) .
>
> I am a bit unsure if we need more details in WP4 (Experiments), but the design og experiments depend on the modelling results in WP1-3, so it is not easy (or wise) to do that.
>
> How do we proceed now?
>
> Cheers
> Tore
---------------------------
> TK:
> The brain sits inside the scull and gets all its information through its sensory systems and must guess what is the most probable causes of these signal patterns.
> (Should we start even more basic – Friston like)
>
> SB:
> We need to start with STRESS
---------------------------
> TK:
> Too strong statement?
>
> SB:
> Yes
---------------------------
> TK:
> Hormones are signal molecules that are very energy efficient broadcasting of messages to all cells in the body (and only the cells the message is relevant for has a receiver (receptor) for the message. Signalling by molecules is also the brains main choice, when speed is not urgent (and electric signals are needed). The endocrine systems cannot bee seen as an independent system from the brain?
>
> SB:
> Of course they are not independent. But physiologists often view them quite separately, there is a clear need to use a holistic whole-organism approach! Not to split it into slices :)
---------------------------
> TK
> Interesting, but have this been explained sufficiently? Since feelings also are concepts made from fuzzy interoceptive signals they can be “wrong” or “false alarms”. Fuzzy interoceptive signals can be interpreted as pain, hunger, fear, etc, when it is adaptive to respond to false models. E.g. it can reduce risk taking or increase feeding opportunities. Since we only can die once, I hypothesise that “false alarms” of potential dangers will be most prevalent (and adaptive)
> SB:
> Very well said

1205 lines of code changed in 1 file:

sbu062 2022-01-26 19:04 Rev.: 12026

Gnatt plot WP4 starts at the beginning

14 lines of code changed in 2 files:

sbu062 2022-01-26 14:11 Rev.: 12025

typo fix

1 lines of code changed in 1 file:

sbu062 2022-01-26 14:06 Rev.: 12024

small fix

1 lines of code changed in 1 file:

sbu062 2022-01-26 14:04 Rev.: 12023

dissemination plan

8 lines of code changed in 1 file:

sbu062 2022-01-26 14:00 Rev.: 12022

small fix

1 lines of code changed in 1 file:

sbu062 2022-01-26 13:58 Rev.: 12021

small fix break line

1 lines of code changed in 1 file:

sbu062 2022-01-26 13:58 Rev.: 12020

small fixes

4 lines of code changed in 1 file:

sbu062 2022-01-26 13:53 Rev.: 12019

started dissemination plan

11 lines of code changed in 1 file:

sbu062 2022-01-26 12:57 Rev.: 12018

word template for CV from NFR

0 lines of code changed in 1 file:

sbu062 2022-01-26 12:55 Rev.: 12017

cv so far

0 lines of code changed in 3 files:

sbu062 2022-01-26 11:46 Rev.: 12016

fixed web forms data after Jarl's comments
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>, Sergei Budaev <Sergey.Budaev@uib.no>
> CC: "Kristiansen, Tore" <torek@hi.no>, Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, Lynne Sneddon <lynne.sneddon@bioenv.gu.se>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: RE: STRESSALGO webforms
> Date: Wed, 26 Jan 2022 08:27:47 +0000
>
> Hi Sergey & al,
> Here are some attempts to make the forms more focussed on the need to improve theories for animal behaviour.
> Jarl

-------------------

> From: Sergey Budaev <sergey.budaev@uib.no>
> To: Jarl Giske <Jarl.Giske@uib.no>
> Cc: Sergei Budaev <Sergey.Budaev@uib.no>, "Kristiansen, Tore" <torek@hi.no>, Christian Jørgensen <Christian.Jorgensen@uib.no>, Ivar Rønnestad <Ivar.Ronnestad@uib.no>, Sigrunn Eliassen <Sigrunn.Eliassen@uib.no>, Lynne Sneddon <lynne.sneddon@bioenv.gu.se>, "Nilsson, Jonatan" <jonatan.nilsson@hi.no>, "Folkedal, Ole" <ole.folkedal@hi.no>
> Subject: Re: STRESSALGO webforms
> Date: Wed, 26 Jan 2022 11:23:50 +0100
> Organization: Universitetet i Bergen
>
> Thanks a lot! One thing: I do not think we can write something like
>
> > Theories of animal behaviour generally neglect stress as a cause for behaviour
>
> Many potential reviewers will be quite annoyed.
>
> S

-------------------

> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: RE: STRESSALGO webforms
> Date: Wed, 26 Jan 2022 10:36:06 +0000
>
> True, it is important to make sure the reader understands that this is about animal behaviour.
> Or is it not? Is it about a model for allostasis? I have been thinking that this is about understanding behaviour.
> But it's your choice, of course.

6 lines of code changed in 1 file:

hje044 2022-01-26 09:48 Rev.: 12015

Added diminishing returns to Appetite-energy, and moved Appetite onto energy intake rather than energy availability. Full rundown in OneNote 2022-2 and 2022-3.

85 lines of code changed in 2 files:

sbu062 2022-01-25 23:20 Rev.: 12014

webforms, sect. 2

8 lines of code changed in 1 file:

sbu062 2022-01-25 22:33 Rev.: 12013

added Hector Zenil on board

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sbu062 2022-01-25 21:51 Rev.: 12012

ikeywords added

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sbu062 2022-01-25 21:48 Rev.: 12011

started filling webforms

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sbu062 2022-01-25 15:06 Rev.: 12010

fixed some vectors, a few were non-linked

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sbu062 2022-01-25 13:56 Rev.: 12009

full re-read and changes, now need fixing refs

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sbu062 2022-01-25 12:34 Rev.: 12008

add some refs to Sneddon

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sbu062 2022-01-25 11:35 Rev.: 12007

more on complexity in H2

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sbu062 2022-01-25 10:26 Rev.: 12006

small fixes, especially from Ivar
> From: Ivar Rønnestad <Ivar.Ronnestad@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: Re: STRESSALGO r11995
> Date: Tue, 25 Jan 2022 09:32:14 +0000
>
> Just a minor correction.
> IvarR

1047 lines of code changed in 1 file:

sbu062 2022-01-25 00:35 Rev.: 12005

Sigrunn Eliassen now in place of Christian Jørgensen

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sbu062 2022-01-25 00:25 Rev.: 12004

fig. 4 include experiment box

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sbu062 2022-01-25 00:03 Rev.: 12003

refit some pics

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sbu062 2022-01-24 23:45 Rev.: 12002

removed orphan/widow control in default style

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sbu062 2022-01-24 23:41 Rev.: 12001

reduce line spacing in default and figure caption styles

231 lines of code changed in 1 file:

sbu062 2022-01-24 23:26 Rev.: 12000

deleted extra indents from H1++

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sbu062 2022-01-24 23:19 Rev.: 11999

integrated Jarl's comments on r11995 with some changes
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: RE: STRESSALGO r11995
> Date: Sun, 23 Jan 2022 14:26:37 +0000
>
> Here are some comments and suggestions, Sergey.
> Jarl
---------------------------------
> Sergey: Although Sigrunn said she was too busy to participate, and Christian has been in the discussion, I still think it is better to include Sigrunn and not Christian. The team is very male-dominated, with only Lynne as female. All you need from Sigrunn is her CV, which she makes for the other projects.
---------------------------------
> Sergey: should the mid-word here (below) be an adjective? predictive homeostasis responses or predictive homeostatic responses?
---------------------------------
> I do not understand the first sentence here (do you need it?)
---------------------------------
> Sergey: find a way to include perspectives and papers of Lynne in this list, also. Second, you argue very much for computation here, but half of all costs in the project are live fish experiments.
---------------------------------
> I do not think you can afford not using every line to its full capacity 😊
---------------------------------
> HERE: CONNECT THIS WITH THE FREE ENERGY PRINCIPLE AND WITH BEING NEAR HOMEOSTASIS.
---------------------------------
> Sergey: the text below, as well as Figure 4 and its legend, does not explain that “the experimental data” also are from experiments with live organisms. Maybe the figure needs to show two separate boxes for experimental challenges; one for simulation experiments and one for live fish experiments. Also the text below should show that half of the costs in the proposal (IMR experiments) are important to the process and outcome of the project.

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sbu062 2022-01-22 00:53 Rev.: 11998

small addition: single currency = affect

1948 lines of code changed in 1 file:

sbu062 2022-01-22 00:47 Rev.: 11997

typo fix

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sbu062 2022-01-22 00:16 Rev.: 11996

use two-rows labels for Marr's levels

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sbu062 2022-01-22 00:16 Rev.: 11995

some revisions here and there, this version will be sent to collaborators

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sbu062 2022-01-21 21:53 Rev.: 11994

cleaner Y on gnatt diagram

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sbu062 2022-01-21 15:55 Rev.: 11993

add fig. 6 Gnatt plotin text

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sbu062 2022-01-21 15:51 Rev.: 11992

added project gnatt graphs

851 lines of code changed in 2 files:

sbu062 2022-01-21 15:15 Rev.: 11991

wp3 fix

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sbu062 2022-01-21 15:11 Rev.: 11990

so far refer to animals

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sbu062 2022-01-21 15:10 Rev.: 11989

first draft for implementation

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sbu062 2022-01-21 13:38 Rev.: 11988

done communication and exploitation

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sbu062 2022-01-21 13:09 Rev.: 11987

merged changes from Jarl, second part
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: RE: stressalgo r11972 - Re: FW: Project participation?
> Date: Fri, 21 Jan 2022 08:30:28 +0000
>
> Here is some more, for the rest of the Excellence section
> -j

385 lines of code changed in 1 file:

sbu062 2022-01-21 12:45 Rev.: 11986

fig. 1 full width

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sbu062 2022-01-21 12:43 Rev.: 11985

set auto hypenation for default style

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sbu062 2022-01-21 12:41 Rev.: 11984

fix figure 1 as suggested by Jarl:
> THIS COMING PARAGRAPH WAS CONFUSING TO ME BECAUSE LEVELS ARE USED FOR DIFFERENT THINGS. THE FIGURE SEEMS TO SORT OUT THREE LEVELS, BUT “LEVEL” SHOULD PERHAPS ONLY BE USED ABOUT MARR’S SYSTEM.
> I SUGGEST THESE CHANGES IN THE FIGURE:
> CATEGORY  TINBERGEN’S CATEGORIES
> TINBERGEN’S QUESTION  TINBERGEN’S QUESTIONS
> MARR’S LEVEL  MARR’S LEVELS
> AND I SUGGEST THAT THE 3 BOXES AT MARR’S LEVELS ARE GIVEN NUMBERS FOR CLARITY: “1: COMPUTATIONAL THEORY” ETC.

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sbu062 2022-01-21 12:28 Rev.: 11983

integrated Jarl's first changes
> From: Jarl Giske <Jarl.Giske@uib.no>
> To: Sergei Budaev <Sergey.Budaev@uib.no>
> Subject: RE: stressalgo r11972 - Re: FW: Project participation?
> Date: Thu, 20 Jan 2022 21:15:27 +0000
>
> An attempt to simplify the reading of the first one and half pages.
> 😊
> Jarl (use track changes to see...)

449 lines of code changed in 1 file:

sbu062 2022-01-21 10:34 Rev.: 11982

add note on refs for readers to not bother with their numerosity

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sbu062 2022-01-20 22:40 Rev.: 11981

small fix again

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sbu062 2022-01-20 22:30 Rev.: 11980

small fix, after sending out

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sbu062 2022-01-20 22:14 Rev.: 11979

title changed to fish

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sbu062 2022-01-20 22:10 Rev.: 11978

done impact

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sbu062 2022-01-20 20:01 Rev.: 11977

impacts started

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sbu062 2022-01-20 17:45 Rev.: 11976

move initial havbruk-targeted stressalgo to `.old`, note hidden dir

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sbu062 2022-01-20 16:58 Rev.: 11975

bold work type and other labels in WPs

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sbu062 2022-01-20 16:54 Rev.: 11974

fig 4 move and enlarge

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sbu062 2022-01-20 15:40 Rev.: 11973

fix fig. 4 need reverse arrow hypothesis to model development

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sbu062 2022-01-20 15:14 Rev.: 11972

done up to W4

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sbu062 2022-01-20 14:52 Rev.: 11971

done up to WP3

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sbu062 2022-01-20 12:56 Rev.: 11970

copied appetite signals for WP3

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sbu062 2022-01-20 11:26 Rev.: 11969

box better look

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sbu062 2022-01-20 11:25 Rev.: 11968

additional arrow published to hypotheses

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sbu062 2022-01-20 11:23 Rev.: 11967

small adjust/move Fig 4

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sbu062 2022-01-20 11:21 Rev.: 11966

add model cycle in Fig. 4

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sbu062 2022-01-20 11:18 Rev.: 11965

fix model cycle

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sbu062 2022-01-20 11:14 Rev.: 11964

refine model cycle, add published data

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sbu062 2022-01-20 10:49 Rev.: 11963

add model lifecycle scheme

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sbu062 2022-01-19 18:37 Rev.: 11962

changes to new H3

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sbu062 2022-01-19 18:16 Rev.: 11961

H3 is non-bayesian emulation of probabilistic mechanisms

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sbu062 2022-01-19 16:16 Rev.: 11960

add `save output` to main help

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sbu062 2022-01-16 10:00 Rev.: 11959

add `fields` bash tool

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sbu062 2022-01-15 00:04 Rev.: 11958

fig borders 0.2

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sbu062 2022-01-14 20:28 Rev.: 11957

modelling strategy: strong inference and pattern oriented

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sbu062 2022-01-14 20:09 Rev.: 11956

delete big arrow that shoiws evolution, nor needed in this context

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sbu062 2022-01-14 20:05 Rev.: 11955

genetic algorithm

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sbu062 2022-01-14 19:56 Rev.: 11954

all figs width 14 cm

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sbu062 2022-01-14 19:47 Rev.: 11953

done hypotheses part

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sbu062 2022-01-14 18:28 Rev.: 11952

rename figs in order

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sbu062 2022-01-14 12:53 Rev.: 11951

H1, with embedded Fig

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sbu062 2022-01-14 12:45 Rev.: 11950

add SC to scheme

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sbu062 2022-01-14 12:37 Rev.: 11949

H1 AHA framework with prediction architecture fig 2

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sbu062 2022-01-14 12:18 Rev.: 11948

fig 2 prediction architecture

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sbu062 2022-01-14 12:07 Rev.: 11947

started hypotheses, copied from 2021 salmon project, for update

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sbu062 2022-01-14 12:01 Rev.: 11946

outline of fish stress and appetite

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sbu062 2022-01-14 11:57 Rev.: 11945

adapted moidel outline for stress

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sbu062 2022-01-14 10:56 Rev.: 11944

add ref Ellis on evolution of stress and costs

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sbu062 2022-01-14 10:45 Rev.: 11943

modelling system was wrong header

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sbu062 2022-01-14 10:41 Rev.: 11942

all subtitles and placefolders addes

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sbu062 2022-01-14 09:04 Rev.: 11941

add HeadURL tag in doc properties

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sbu062 2022-01-14 09:02 Rev.: 11940

ref to Del Giudice

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sbu062 2022-01-14 00:27 Rev.: 11939

theory not hypothesis

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sbu062 2022-01-13 23:43 Rev.: 11938

added on existing models and advantage of fish

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sbu062 2022-01-13 18:00 Rev.: 11937

revert notes from r11934, and fig.1 to bottom of page

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sbu062 2022-01-13 17:53 Rev.: 11936

figure 1 to bottom of page

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sbu062 2022-01-13 14:15 Rev.: 11935

striped notes, to send to Tore and Lars

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sbu062 2022-01-13 14:13 Rev.: 11934

small changes before sending to Lars and Tore, need to delete notes on WPs

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sbu062 2022-01-13 10:38 Rev.: 11933

notes on WP2

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sbu062 2022-01-13 10:10 Rev.: 11932

Fig. 1: levels under focus grayed

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sbu062 2022-01-13 09:42 Rev.: 11931

add greyed boxes for focused levels

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sbu062 2022-01-13 09:07 Rev.: 11930

retag figure 1, added Goldstein old ref on allostasis

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sbu062 2022-01-12 16:49 Rev.: 11929

regenerated svg after change of align

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sbu062 2022-01-12 16:44 Rev.: 11928

need new line without align

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sbu062 2022-01-12 16:39 Rev.: 11927

white space only

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sbu062 2022-01-12 16:36 Rev.: 11926

additional small fixes

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sbu062 2022-01-12 14:19 Rev.: 11925

Feynmann note

26 lines of code changed in 1 file:

sbu062 2022-01-12 14:07 Rev.: 11924

done levels of analysis, text and fig

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sbu062 2022-01-12 13:27 Rev.: 11923

generated svg: `dot -Tsvg draw-causes-levels.dot > draw-causes-levels.svg`

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sbu062 2022-01-12 13:26 Rev.: 11922

added figure for Tinbergens Q and Marrs L

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sbu062 2022-01-12 13:17 Rev.: 11921

more complete scheme

17 lines of code changed in 1 file:

sbu062 2022-01-12 12:48 Rev.: 11920

scheme for integrating Tinbergen's four questions and Marr's levels of analysis for mechanism
{{{
dot -Tsvg draw-causes-levels.dot > draw-causes-levels.svg
}}}

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sbu062 2022-01-11 22:44 Rev.: 11919

format only, no content change

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sbu062 2022-01-11 22:42 Rev.: 11918

modifications after Jarl's first round of comments

1. You may need to add "in animals" so that the proposal is not sent to some medic who does not understand all this animal nonsense.

2. I think you also here need to state clearly that you will study animals. Maybe say that stress is a gigaproblem for the modern western population, and therefore has been studied by a hoard of shrinks who have ignored the long evolutionary background. But thanks to these shrinks we now have a pile of empirical and theoretical studies that we can "take home": it can be set to use on all those animals in and for whom stress evolved.

3. Rather: Growth and survival

4. I would tread very carefully with mentioning any sort of "applications" here. It is legal to mention them later in the document (section 2.2 Potential for societal impact of the proposed research). Here I would rather say that stress impacts activity, space use, feeding, growth, mortality etc.

5. You do not explain why this is an urgent need, you just state it. And maybe it is a too strong statement. What if you rather said that it would be valuable for the study of most non-human animals to develop a theory that contains a mechanistic base?

305 lines of code changed in 1 file:

sbu062 2022-01-11 22:18 Rev.: 11917

small fixes before JG and TK reply

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sbu062 2022-01-11 17:29 Rev.: 11916

refer to revision

30 lines of code changed in 1 file:

sbu062 2022-01-11 17:27 Rev.: 11915

added keywords

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sbu062 2022-01-11 17:26 Rev.: 11914

other small fixes

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sbu062 2022-01-11 17:11 Rev.: 11913

add on hormones

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sbu062 2022-01-11 16:46 Rev.: 11912

small change

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sbu062 2022-01-11 16:39 Rev.: 11911

done objectives and basic approach

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sbu062 2022-01-11 00:12 Rev.: 11910

done algorithms and dynamical systems, now objectives only remain to be done

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sbu062 2022-01-10 14:06 Rev.: 11909

levels of analysis and algorithmic

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sbu062 2022-01-10 13:15 Rev.: 11908

done bayesian brain and active inference

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sbu062 2022-01-10 07:23

small wording fix

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sbu062 2022-01-10 00:16 Rev.: 11905

more on allostatic load

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sbu062 2022-01-08 00:14 Rev.: 11904

small changes

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sbu062 2022-01-07 13:59 Rev.: 11903

started modelling framework

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sbu062 2022-01-07 13:33 Rev.: 11902

added allostatic regulation aragraph

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sbu062 2022-01-05 14:04 Rev.: 11901

Fripro-21: new general intro started to modify

235 lines of code changed in 1 file:

sbu062 2022-01-05 13:37 Rev.: 11900

better name

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sbu062 2022-01-05 13:36 Rev.: 11899

need project file separate from first draft that is archived

0 lines of code changed in 1 file:

sbu062 2022-01-04 23:14 Rev.: 11898

small text changes

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sbu062 2022-01-04 22:45 Rev.: 11897

refs ai and causality

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sbu062 2022-01-04 14:25 Rev.: 11896

refs on machine vision

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sbu062 2022-01-04 14:09 Rev.: 11895

refs on fecal cortisol

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sbu062 2022-01-04 11:55 Rev.: 11894

more refs added

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sbu062 2022-01-04 10:20 Rev.: 11893

APA references easier to work with

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December 2021 »

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