Review: Wolfram Research Publicon

Product Name: Publicon
Company: Wolfram Research
URL: http://www.wolfram.com/products/publicon/index.html
Category: Document Processing
Price: $149
Requirements: OS X
Rating: 2 bounces - Lack Luster

A Few Months With Publicon

Publicon is a new scientific word processor from Wolfram Research, the makers of Mathematica. It has built in equation-editing, cross-referencing, and footnote/reference management. Publicon produces output in a variety of formats including PDF, XML, HTML + MathML, and LaTex. If you have used Mathematica then Publicon's interface will be very familiar. If you have not used Mathematica, it may require some getting used to. Publicon is not like other word processors on the market, it has more in common with Framemaker and Ragtime than it does with Word. The current 1.0 release of Publicon shows great promise but at the present time it feels more like beta software than a polished software product. Hopefully, Wolfram will continue to improve Publicon so that it can reach its full potential.

PACS numbers: PACS

I. Introduction

Publicon from Wolfram Research is designed for producing technical documents. It uses their Mathematica engine for both its WYSIWYG output and document management tasks. Mathematica is a very mature program that can perform complex mathematical calculations. As a long time user of Mathematica, it was with great enthusiasm and great expectations that I agreed to review Publicon. I had been a long time user of Framemaker, but since Adobe has decided to end-of-life Framemaker on the Macintosh, I had been seeking a replacement. I decided that the best way to test Publicon was to use it, rather than Framemaker, to write all of my scientific documents for a three month period.

Publicon does contain most of the features necessary for scientific document publishing. In fact, I found that I did not need to use MathEQ for equation editing or EndNote for Reference management, as both of these features are built in to Publicon. It has a variety of Style Sheets that are preformatted for styles expected by the American Physical Society, the American Mathematical Society, and BioMed Central. You can edit or create your own Style Sheets. Output is also available in a variety of formats. Publicon allows the author to chose from PDF, LaTex, XML, XHTML + MathML, HTML, and as a native notebook format. There is also an option to save as HTML for Microsoft Word. The primary means of entering text into a Publicon document is through the use of what I will refer to as Mathematica cells.

II. Document Structure

The first step in creating a document is to select the Style Sheet that you are going to use in the document. The first two windows that pop up are a text window (Figure 1) and the Formatting Palette (Figure 2). The text window has the default sections necessary in the particular format that you select. In the American Physical Society (APS) document window, the Title, Author, Date, Abstract, PACS number, Section 1 with Text, and an Appendix are all ready to be populated with your text. On the left side of the document window are a large number of brackets. These brackets indicate individual Mathematica cells. In a Publicon document, everything is entered into a cell. In fact, each individual paragraph is its own cell. This means that text is not free-flowing. One consequence of this is that you cannot select and delete between two paragraphs. This was actually the most difficult thing for me to get used to. When I write, I tend to “overparagraph” a bit. Often when I go back through the document, I combine two paragraphs into one. Because they are two separate cells, I had to copy one cell into the other and then delete the second cell. The cell concept does make it easy to add Document Sections with the Formatting Palette.

Figure 1: Blank American Physical Society Document

Figure 2: American Physical Society Formatting Palette

The Formatting Palette is used to add Figures, Equations, Sections, Tables, Cross-References, and References to the document. My only complaint with the formatting palette is that there is a slight inconsistency in the way that buttons operate. The majority of the buttons in the Formatting Palette insert a new object into the document. However, some of the buttons reformat the current cell. The problem is that if you accidentally reformat the current cell, there is no easy way to undo it. The Undo item in the Edit menu does not undo this mistake. Other than that it is very easy to use the Formatting Palette to give your document the structure that you want.

Figure 3: Document With Text

Figure 3 shows a document with two Sections and the cell structure of each. The first section has three cells associated with it, the Heading and the two paragraphs. The brackets allow you to determine the organization of the document. From Left to Right, you can see that the three individuals cells fall with the next bracket denoting the cell containing the section. The outermost bracket contains both sections and denotes the body of the document. Careful examination of Figure 3 shows that it is actually this document that is depicted. Obviously, all of the structure in the text window is not present in the final output. The document formatting is not performed until the document is either printed or exported to its final output form, in this case, HTML. In this regard, while you see WYSIWYG equations, figures, etc. on-screen, the on-screen image really doesn’t indicate the final output. The programmers at Wolfram took care to make the on-screen image quite similar to the final output but it is not a one-to-one correspondence. You can modify the screen output by using the Screen Environment Menu but even in the best case it is not the exact output that you get by printing.

One of the unusual consequences of this lack of correspondence between the on-screen and final output is that it is very counterintuitive to change and even to observe the printing parameters (margins, spacing, alignment, etc.) of a given paragraph. These parameters are changed in the Preferences Menu of the Application. One can eventually learn to accept this method of setting parameters but there is one very dangerous caveat to keep in mind and one that Wolfram must fix. The preferences menu defaults to GLOBAL change as seen in Figure 4. In my experience I usually utilize the defaults and occasionally want to change values for a single paragraph. I have forgotten to change from global to selection while quickly making a change. This effects every paragraph in the document and every document utilizing that Style. That is a big mistake, again with no easy method of undoing. I had to trash my Publicon preferences and reinstall that application to undo that one. I would hate to have to learn how to recover from that on a Windows box. While the need to use the Application Preferences to change the parameters of a given paragraph is a bit convoluted, it does afford a maximum of control over the final output.

Figure 4: Preferences Menu For Publicon

III. Equations, Tables, and Figures

One of the areas where Publicon really shines is in the formatting of Equations and Tables. Both Equations and Tables can be added by simple clicks on the Formatting Palette. Once created the Typesetting Menu (Figure 5) is used to create either inline or separate equations. Inline equations show in the line of text as in the following sentences. The reduction of U(VI) to uraninite (, ) could be a more effective approach for uranium immobilization. Einstein proved that the Energy of a particle with mass (m) and momentum (p) is given by the equation,  . Equations can also be of the stand alone variety. The time-independent Schrodinger equation is given in Equation 1.

(1)

The equation editor also has very nice templates for the creation of formulas and equations for use in chemistry.

(2)

Having been a long time Mathematica user, I find the equation editing interface very simple to use and quite effective in producing publication quality images. Novice users should have no difficulty learning the editing interface. I discovered a couple of issues with the creation and editing of equations is that should be fixed. First, it is difficult to select inline equations for editing. The work around for this was to always select from left to right, as a right to left selector, I had some difficulty adjusting to this particular feature of the software. The other unusual bug occurs when pasting a formula into a subscript, occasionally, the software forgets what it is doing and pastes in Mathematica programming text into the document. It is easy to work around both of these bugs, by selecting backwards and by not pasting into subscripts. One required me to change my habits and the other added work by making me retype equations that were already entered. However, it is difficult to complain too much in this area as the output equations are exceptional.

Figure 5: The Typesetting Palette Containing Equation, Text, and Table Formatting Parameters

Table I shows an example of a 3 by 5 table with column headings and a table description. The Formatting Palette is used to create tables. The new table is readily customized with the Typesetting Palette. With the Typesetting Palette, it is easy to add rows and columns. Table selections can be spanned and unspanned. As with equations, beautiful tables can be created with.

Table I. The observed reaction rate constants of a pseudo-first-order rate equation are given.

Figures are also added into a Publicon document through the Formatting Palette. One click adds a caption and a box as a placeholder for the image. A filename selection window pops up to allow for image selection. Most common image formats are supported by Publicon. I have typically used either TIFF, JPEG, or EPS files. In this review, all of the images were TIFF files. Each image is imported into its own cell. Images can be resized within a cell by selecting the images and using the selection points to either enlarge or shrink an image. Obviously, the higher quality image used, the better the final Publicon output. One feature that should be added is the ability to add figure subnumbering. Often images contain part

(mM) Rate Constant k () of the Linear Fit

0.83 5.90× 0.96

1.46 1.34× 0.95

2.09 1.84× 0.96

4.75 2.73× 0.96

6.83 3.86× 0.97

s a, b, c, etc., it would be useful to be able to add a Figure X(a) for example.

IV. References

Publicon has its own reference database similar to that of EndNote. References are added to the database by the popup window shown in Figure 6. When references are initially placed into the publicon document, they appear in a placeholder format that looks like this: [Payne2004]. References are placed into the document by selecting from a list of the database. It is possible to search the database. Currently, the database can be searched by a Text Key, 1st Author, and Title. It would be nice if the search could be expanded to include a search by any author as often the last author is the better known individual. Once the reference has been found, a simple click places it into the document.

In order to create the Reference section of the document and replace the placeholders with citation numbers, the Gather Backmatter button in the Formatting Palette (Figure 2) must be used. This procedure creates the standard Reference section. Publicon places all fields in the Reference section whether they are populated in the database or not. This was a decision made by the creators of Publicon. They felt that this would inform the author of missing information that should be located and included in the database. I have the opposite view, I feel that missing information should not be by default included in the Reference section. If a journal number is not included in the database along with the volume number, it should not be added into the Reference section. By including these empty values, the author must delete a large number of empty placeholders. It is nice to have the database included in the document processing application rather than needing to use a second application.

Figure 6: Reference Database Window

V. Camera Ready

One of the biggest shortcomings of Publicon, is its inability to produce “Camera Ready” documents. Many conference proceedings require submissions in specific formats that are ready for immediate publication. These formats are known as “Camera Ready.” Typically, they are two column formats with images sized to fit one or both columns. Publicon currently does not have the ability to output anything other than one column text. This is a glaring omission in an application geared towards scientific and technical document creation.

VI. Conclusions

Publicon 1.0 is good first release. It shows great promise as an application for scientific document processing. It contains many of the necessary features that one would expect in a scientific word processor. The equation editor is first rate. The bibliographic database is also quite good. As detailed above, there are a few minor issues with Publicon that make this release seem like beta software rather than a full release. There are two major issues that make it difficult to recommend Publicon as a primary scientific word processor. By having the Preferences default to a Global state, it is too easy to accidentally ruin all of your Publicon documents with one inadvertent strike of the return key. Second, by not including a means to create “Camera Ready” documents, it forces authors to keep another word processor around to create publication ready documents. I believe that the vast majority of people want to use a single word processor for all of their document creation. Unfortunately, Publicon is missing features that could allow it to be my only word processor. That said I have purchased two additional Publicon licenses. I am very comfortable with the Mathematica cell interface. I am quite pleased with the equation editing and output from Publicon. Wolfram Research has indicated to me that they are working on a means of providing multi-column output. I see a program that with some effort by Wolfram could make me forget that I ever used Adobe Framemaker. I hope that Wolfram will continue to forge Publicon into a great scientific word processor because it is not there yet.

APPENDIX A: Example

I have included a full example document that was created with Publicon. This document showcases many of the features found in Publicon.

- Jeff Terry

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