Wilfrid Rall Archive: Detailed Contents of Research Notebooks

Tools for identifying, searching and retrieving topics in a notebook
Most of the notebooks lack a built in page numbering sequence, so several tools are provided for accessing the topics. For archival purposes, each page has been scanned as a pdf. The archival sequence of pdfs, with its own numbering sequence of the pages, is provided for the clearest reproduction of each page.
For the index, each page has been reviewed by one or more curators to identify and define the topic covered, which in many cases involved Rall creating new terms and concepts. Each scanned page of written material is approximately a 1 MB pdf, which makes a slow process for searching the pdfs directly. 
The quickest way therefore to search the Notebooks is provided by a webbased preview tool: at the bottom of the webbased image move through the pages by moving the circle on the scale, or by clicking on the forward and back arrow heads. In the index the page number in this web preview sequence is indicated by an initial p.#. The link is accurate to within one or several pages, depending on any ambiguity and extent of the topics spread over several pages, which in the preview can be quickly determined.
In most of the notebooks (except Notebooks 1, 2 and 6) Rall entered his own numbering sequence with a number # in the upper right hand corner of the page, indicated by wr# in the index. In Notebook 6 each page comes already numbered, indicated by b# instead of wr#. The surest way to identify the page of a topic is indicated by the date that Rall entered for the entry, in the upper left hand corner of a page.
Thus, a full index entry reads: page (p) in preview web sequence; page (wr) in the Rall notebook; date of entry in the Rall notebook; title or topic covered on that page(s); comment by curator in italics; entry of special interest in bold.
Example: Notebook 4 p.121 wr58 8/25/64 Action potential computations: active vs passive dendrites. First HodgkinHuxleylike action potential in a compartmental model of a dendrite 
Notebook 1 19591962.
Early computer program development. 
Early program development with Mones Berman, Ezra Shahn, Marje Weiss and Jeanne Altmann, on the IBM 650 and HONEYWELL 800.
 p.6 Aug 1960. Computation Procedures: somadendritic extracellular fields.
[table of contents] 
Notebook 2 July 1962Nov 1963.
Begin development of computational models for epsps and ipsps in motoneuron dendrites with Karl Frank group at NIH; first presentation of the Rall method in Dec 1962; begin work on olfactory bulb neuron models with Gordon Shepherd; begin a HodgkinHuxley like action potential model.
 p.6 of 175. (web) Begun 7/62, retrospective to 5/63 “Compartmental Computations Record”
p.8 7/17/62 Compute branching dendritic compartments
[Sept 1962 Gordon Shepherd arrives]
p.21 9/18/62 Compute equivalent cylinder of motoneuron dendrites
p.30 11/2/62 New Bifurcating Tree Series
p.36 11/21/62 Excitation in periphery
p.38 11/21/62 Inhibition for different sites
p.46 11/15/62 Equivalent cylinder: ten compartments, excitatory and inhibitory spatiotemporal integration
p.50 Dec 1962 Break for Trip to L.A. & Seattle to present material. [First presentation of compartmental approach at Ojai Symposium]. Manuscript written in Feb & Mar 1963
No more computations until May 1963
p.118 7/1/63 Explore unequal compartments
p.120 7/2/63 Begin to test epsp & ipsp summations for different locations in branching dendritic tree
p.122 7/3/63 Begin to explore use of qdependence to mimic an impulse. Preliminary runs of an action potential model.
p.140 7/22/63 (Action Potential) Impulse model, using Q .
Loose Papers
Problems of using Mone’s program for my problems when compartments are not all of equal size: binary branching
p.162 11/15/63 New model for photoreceptor kinetics which embodies some of the spatiotemporal Ge notions of my dendritic tree model
[table of contents] 
Notebook 3 19631964.
Work on computational model of action potential invasion of mitral cell axon, hillock, soma and dendrites; compare passive and active mitral cell dendrites; reconstruct recording arrangement and field potentials.
p.4 of 240 11/6/63 Computations of Propagated Activity Record. This record begun Nov. 6, 1963, but retrospective to Qdependence notes in other notebook (July 1963). Table of Contents on p. 5
Mostly olfactory bulb study with Gordon Shepherd. [Not shown: development of a model of extracellular recording based on the “potential divider” effect of the recording electrodes, to accurately analyze the summed extracellular recordings from different layers of the olfactory bulb.]
Start development of a simplified HodgkinHuxley action potential model, to model antidromic invasion in a chain of compartments representing the axon, soma and dendrites of a neuron (mitral cell), to compare active vs passive spread of the action potential into the soma and dendrites.
p.6 wr1 8/5/63 Began to develop new program series, based on success of BermanWeiss program
Explored a compartmental model to mimic action potential in a single compartment.
Purpose was to compute for active and passive chain and plot results. [Ed. this was apparently the first implementation of a HodgkinHuxley like action potential in a digital compartmental model].
p.60 wr28 12/4/63 Now begin to roughout mitral axon, soma, dendrites (active/ passive)
1964
p.110 wr53 1/10/64 Axonsoma spike delay [a first in computational neuroscience, to compare with electrophysiological recordings].
p.134 wr65 1/22/64 New idea of stochastic model of neuronal branch pattern, to deal with loss during sectioning.
p.138 wr67 1/27/64 Model of antidromic hillocksoma delay and block.
p. 142 wr69 1/30/64 Conclusions on comparing antidromic mitral invasion and extracellular potentials., which is necessary for fitting mitral cell data …
p.158 wr77 2/5/64 Working hypothesis: mitral cell extracellular potentials suggest hot short passive dendrites or cool long active dendrites. Gordon agrees (p. 162)
p. 164 wr80 2/19/64 Hypothesis: Both giant extracellular spike. & a nonchemical epsp could be explained by lowresistant synaptic plaque.
p.170 wr83 2/20/64 “revising paper on Aitken’s data with help of Gordon”: “problem of trunks lost or obscured by the soma”.
p.182 wr89 3/4/64 “Stock taking of Papers to be Completed in Coming Year”.
p. 184 wr90 3/10/64 Problem of core conductance between synapses and hillock.
p. 186 wr91 3/10/64 Dick Fitzhugh about Ojai paper: adding active axonal nonlinearities to E depolarization and J hyperpolarization.
p. 188 wr92 3/11/64 van Buren. Motoneuron recordings advice.
p. 190 wr93 3/11/64 impedance and clamp response of my impulse model.
p. 198 Computation People.
p. 200 Loose papers. Computer printouts
[table of contents] 
Notebook 4 196364.
Perspectives on modeling; analyse the antidromic action potential and extracellular potentials; predict dendrodendritic synaptic interactions between mitral and granule cells generating feedback and lateral inhibition; new concept of Generator of Extracellular Current. 
p.5 6/19/63 (mostly 1964) Research Diary. Diary purpose.
p.7 wr1 2/13/62 Project list [pdf] [web viewer]
p.911 wr23 3/11/64 Summaries of Books 1, 2, 3
p.12 Aitken note (see also preceding page)
p.13 wr4 3/12/64 Dendritic branching
p.14. People to write to
p.15 wr5 3/12/64 Papers to be completed
p.17 wr6 3/18/64 Synaptic contact areas; Kathryn Thomas
p.20 Anodal break question p.21 wr8 3/26/64 Rashevsky lunch; stimulated impulse model testing
p.25 wr10 3/30/64 Aitken motoneuron letter
p.27 wr 11 4/3/64 with Gordon discussed Aitken data about L/lambda
p.29 wr12 4.7.64 Jose conversation Laplace Fourier transforms; Bode diagram
p.35 wr15 4.15.64 Program modified for giant e.c. spike; spike upslope p.3663 wr1664 4/16/64 Completed ms with Gordon; computation problems
p.65 wr30 5/11/64 Perspectives on kinds of modeling problems
p.67 wr31 5/18/64 Betty Garber: gave talk; 3d dendritic branching calculations
p.73 wr34 5/20/64 Stock taking; discuss Gordon’s records re ? simulation
p.7590 wr3542 5/21/64 5/22/64HH kinetics of membrane patch; voltage clamp, etc.
p.91 wr43 5/22/64 problem of getting steady state with simplified HH model
p.93106 wr4450 5/25/64 Electrical units used in HH model test.
p.108 wr51 6/6/64 Simulating AB break in the antidromic action potential
p.109 wr52 6/10/64 – 8.12.64 Major interruption of research; review
p.111115 wr53 8/12/64 Fitzhugh HH suggestions (see loose pages below)
p.117119 wr5557 8/22/648/24/64 “Discussed late potential… with Gordon today." Thoughts about dendrodendritic synapses between granule cells & mitral cells of olfactory bulb. [pdf]
p.121 137 wr5866 8/25/649/1/64 Action potential computations: active vs passive dendrites; e.c. potentials; analysis of geometric load on antidromic action potential
p.139 wr67 9/2/64 granule cell model simulations; hot & cold kinetics
p.141 wr68 9/3/64 talk with Stefanis (St. Eliz) & Gordon: Betz cells; e.c potentials; antidromic invasion depends on USD/USA.
p.143 wr69 9/3//64 next page: Gordon likes USD/USA = 40, intuitively in preference to 80
p.147 wr71 9/11/64 Snowed under with calculations and talking with Gordon about the writeup
p.149 wr72 9/11/64 Granule cell E.C. Potential Model: many runs
p.159 wr77 9/11/64 active vs passive dendrites; Fitzhugh thoughts
p.160 wr78 9/11/64 Yesterday Gordon and I discussed writeup; importance of concept of GEC (Generator of Extracellular Current) in contrast to recorded e.c. potential wave; definitions of abbreviations
p. 163 wr79 9/11/64 prepare paper; comparing deep and superficial e.c. waves in periods I, II, and lll
p.167 wr81 9/11/64 Detailed comparison of model and experimental e.c. potentials
p.175 wr85 9/15/64 next page: diagram of radial cone of e.c. current in olfactory bulb
p.181 wr88 9/16/64 mitral axon spike e.c. current; apply d3/2 rule
p.183 wr89 9/16/64 refer back to p.29 of Book 3: mitral GEC and potential divider effect
p.188 wr92 9/17/64 Consider active vs passive; axon e.c. currents like in oil; compare Gordon’s records
p.190 wr93 9/17/64 simultaneous invasion of primary and secondary dendrites
p.192 wr94 9/17/64 Conclusion: must interpret deep to superficial e.c. recordings with potential divider effect
p.194 9/17/64 NIH Computer Systems support team End of Book 4.
[table of contents] 
Notebook 5 196465.
Modeling somadendritic interaction; Eccles after dinner speech on scientific culture and Popper reminiscence; Perkel model; emphasize the value of a simpler HH model.
p.28 of 204 wr12 9/28/64 first completely successful extracellular run
p.62 wr29 10/6/64 Explore somadendritic action potential block and facilitation of passive and active dendrites.
p.88 wr42 10/19/64) Drafting paper.
p.108 wr52 10/26/64 gradients show current from dendrites to soma
p.112 wr54 10/26/64 GMS leaves for Stockholm.
p.114 wr55 10/26 /64 comparisonof mitral, axons, granule wave potentials.
p.132 wr64 11/26/64 Eccles after dinner speech; Popper reminiscence. conflicting priorities. Perkel: A DigitalComputer Model of Nerve Cell Functioning.
p.140 wr68 11/20/64) Conflicting priorities. Perkel: A DigitalComputer Model of Nerve Cell Functioning.
p.154 wr75 12/2/64 Value of the simpler HodgkinHuxley model. Resolve to write papers.
p.166 12/8/64 p. 80 Mitral paper outline.
[table of contents] 
Notebook 6 1965 JanJuly.
Importance of concepts in science; notes on Hodgkin lecture; breakthrough finding by Reese and Brightman of dendrodendritic synapses confirming prediction; work on papers of Frank, Rall, Nelson, Burke, Evans, Smith on motoneuron dendrite synaptic integration.
p.8 1/5/65 Outline of projects. Send abstract with Gordon on olfactory bulb model for 1965 IUPS (Int. Union of Physiol. Sci.) Tokyo.p.12 1/12/65 Concepts vs Equations. Control Theory. Reading “Adaptive Control Processes” by Richard Bellman. “…he emphasizes some points I have often emphasized. “…concepts play a role equally important with that of equations, and the construction and interpretation of mathematical models is of even greater significance than the solution of the particular equations to which they give rise.” [GS: We touched on this in our discussions, because it was the justification for him as a mathematician and for me as a non mathematician to work together to develop both mathematicallybased and experimentally based neuron models.]
p.14 1/13/65 “Optimization Theory and the Design of Feedback Control Systems.” Charles W. Merriam III
p.22 b3 1/14/65 Hodgkin lecture: detailed notes.
p.24 b59 1/15/65 Ted Lewis: examples where theory predicted experiment.
p.36 b17 1/17/65 further analysis of active vs passive olfactory bulb dendrites
p.44 b25 2/3/65 Phil Nelson & van Buren motoneuron.
p.102 b83 3/2/65 prepare Cal Tech lectures. Returned 3/12/65
p.106 b87 3/15/65 Olfactory bulb: Reese seminar: breakthrough finding of dendrodendritic synapses by Tom Reese and Milton Brightman. [Wil immediately provided a detailed explanation of how they confirmed our prediction. He wrote me a long letter about it on 3/15/65]
p.108 b89 3/16/65 Motoneuron: Spent afternoon with Kay Frank, Phil Nelson, Bob Burke, Ted Evans, Tom Smith: detectability at soma of dendritic epsp conductance change. Wil models of peripheral epsp (3/16 – 3/22).
Index details later
p.180204 b157181 4/16/65  5/14/65 Discussion of questions raised about our model by Reese & Brightman cf. paper by Hirata.
p.214 b191 6/15/65 GMS visiting NIH to finish first paper with Wil and Reese. Science rejects ms. Submit instead to Exptl Neurology: Rall, Shepherd, Reese, Brightman 1966.
[table of contents] 
Notebook 7 8/3/1965 – 12/15/1965.
Wide consultation with many colleagues; Eccles lecture on cerebellum; intensive computations for motoneuron papers throughout the notebook;“Cortical Potential Field Theory” ms.

p.6 wr2 8/3/65 Preparations for abstract in Tokyo. Finalize first dendrodendritic paper with Tom, Milton and Gordon. Return to work on motoneuron. Rall wide consultation.
p.8 wr6 8/4/65 slides for Tokyo. 9/20/65 Back from Tokyo
p.12 wr8 9/24/65 Per Anderson. Biophysics of multiple spines.
p.14 wr10 9/27 Work on motoneuron papers
p.26 wr22 9/30/65 Eccles lecture on cerebellum.
p.28 wr24 9/30/65 motoneuron epsp
p.41 wr36 10/6/65 “Cortical Potential Field Theory” ms.
p.48 wr44 10/12/65 Note on Time Constant of NonUniform Decay
p.64 wr60 10/19/65 Computation Series Recapp.96 wr92 11/4/65 Computation memo for Frank, Smith, Nelson, ?
p.102 wr98 11/9/65 Spent all day with K. Frank, Tom Smith, Phil Nelson, Bob Burke on motoneuron biophysics. Many pages of calculations.
p.130 11/19/65 Exp. Neurol olfactory bulb galley proofs.
p.164 wr164 12/8/65 Fruitful meeting with K. Frank, Phil Nelson & Bob Burke. Minis and evoked epsps.  [table of contents]

Notebook 8 2/15/65 – 6/27/66.
Continued work on motoneuron papers; thoughts on mathematics approach in science; compartmental vs continuous systems; meaning of “model”; neuroanatomy declining; theoretical and experimental approaches; how to write a good book.
p.12 wr6 12/16/65 K. Frank discussed plan of four motoneuron papers. Difficulties of overlap.
1966
p.34 wr30 1/4/66 Summary last 2 months computations
p.39 wr35 1/5/66 Lux & Pollen pyramidal cell basal dendrites
p.40 wr36 1/5/66 letter to Gordon on olfactory review with Ottoson.
pp.7882 wr7378 1/17/66 Discussion of mathematics approach in science with Jose. Newton & Leibniz. Fundamental solutions. Compartmental vs continuous systems. Meaning of “model”: general, particular, specific.
p.86 wr81 1/20/66 Karl Frank suggested a Symposium on Mathematics Models for Neurons and Synapses before the Atlantic City Fed meetings
p.88 wr83 1/25/66 Key to success: omit figures?
p.89 wr84 1/25/66 outline of paper on new models.
p.90 wr86 1/27/66 gave Biophysics Lab seminar
p.90 1/27/66 polish off the paper with Gordon? computational model elsewhere?
p.90 2/3/66 get together with Phil Nelson on 5 motoneuron papers. Mike Bennett.
p.112 2/16/66 Computed Synaptic Potentials ms.
p.120 wr116 2/22/66 For April 11 at Neurophysiology Club at Atlantic City
p.122 wr118 2/25/66 “flood of reprint requests for dendrodendritic paper”.
p.128 wr124 3/2/66 Rasmussen comments on neuroanatomy decline and Cajal Club.
p.134 wr130 3/7/66 Reese stopped by with dendrodendritic reconstructions.
p.146 142 3/23/66 Ainsley Iggo. Burke. Equalizing time constants. Formulation: Theoretical vs Experimental: Levels: qualitative, semi quantitative, quantitative: Thoughts.
p148 wr143 3/24/66 Mismatch between expt and theory
p.146 3/25/66 medical student Roger Nicoll visit, discussed hisolfactory bulb experiments. “Seemed pretty bright and up to date …”
p.152 wr148 3/30/66 presentation to the Scientific Council of NINDB.
p.156 wr152 4/13/66 Atlantic City Symposium. Conversations with many colleagues. Larry Goldman. Talk at College Park. Katz comments.
p.157 wr153 5/2/66 first transient solution for the finite cylinder
p.158 wr154 5/2/66 Slides for College Park talk: mostly Obulb
p.166 wr161 5/17/66 Working on EPSP & Bulb papers. Neurophysiology in Theory and Practice Science: How to write a good book.
p.167 wr162 5/17/66 to p.194 wr190 6/24/66 K. Frank, Phil Nelson, Bob Burke joint paper work. Many computer runs.
[table of contents] 
Work in progress:

Notebook 9 6/27/66 –11/15/67.
Work on motoneuron papers; positive response to dendrodendritic story; submission of 5 motoneuron papers; finalized second dendrodendritic model paper on model details; EcclesRall symposium on New Developments in Vertebrate Synaptology.
[table of contents] 
Notebook 10 5/6/68 to 2/11/70.
Work on dendritic spines with John Rinzel; role of mathematical theory in neuroscience; response to Kuffler report which makes no reference to mathematics or biophysical theory.
[table of contents] 
Notebook 11 11/10/69 to 3/9/72.
Boulder meeting; dendritic neuron theory ms; first annual meeting of Soc for Neuroscience (Rall was on the first council); Rall makes an extensive list of new generation of Neural Modellers, Biophysicists and Theoretical Biologists.
[table of contents]