NoteBook Discussion Forums: Special Interest Communities - NoteBook in SciTech

Import functionality (commented by davidpost)

davidpost — Mon, 25 Jan 2010 19:44:41 +0000

I also use MathType and find it good. Presently I also save the file and paste it into Notebook. It is okay but it would be nice to be able to simply click on my Notebook entry and have it open up in MathType so that I can edit my equations.

Regards
David

Suggestions for using Notebook to study for MCAT? (commented by Clare )

Clare — Fri, 11 Dec 2009 17:57:32 +0000

I don’t think there is a private message function but you can contact me through the website on my profile.

Suggestions for using Notebook to study for MCAT? (commented by SirIsaacNewton)

SirIsaacNewton — Fri, 11 Dec 2009 15:36:52 +0000

I am a medical student using Notebook for organizing my lab notebook as well as my notes from class. I love it. Studying for the MCAT now that is a different story. I can’t help you there but wish you the best of luck. If you private message (if that is possible?) me I can tell you a little about my institution and give advice along the lines of applications.

Import functionality (commented by meitnik)

meitnik — Mon, 07 Sep 2009 23:31:52 +0000

humm, how would LaText work with Nb. I have the request to support Math symbols better. I am using Mathematica Home Edition myself. I would love a link back via MathLink or support for MathML via WebKit.

Import functionality (commented by peter lindsay)

peter lindsay — Sun, 06 Sep 2009 21:38:25 +0000

Don’t use mathtype, use LaTeX instead.

Requirements for an electronic lab notebook system (commented by Clare )

Clare — Thu, 03 Sep 2009 20:17:11 +0000

For chemical/water resistant pens- I really like uniball signo http://www.uniball-na.com/main.taf?p=2,2,3.

For the centrifuge tubes I like VWR markers http://vwrlabshop.com/vwr-lab-markers/p/0011283/

For really important samples I use http://www.emsdiasum.com/microscopy/products/label/tough_tags.aspx?mm=23 Tough Tags (the plain white ones).

Requirements for an electronic lab notebook system (commented by Higher Than the Sun)

Higher Than the Sun — Mon, 24 Aug 2009 16:39:37 +0000

Clare, in theory one could use Time Machine to keep track of precision changes to the notebook. It isn’t a perfect solution, of course, and in order to track all changes it wouldn’t work very well, as Time Machine is designed to cull backups over time. Another solution would be to continually archive your NoteBook (print > save as PDF, or export as HTML in order to get embedded files as well), which would generate snapshots in time. That’ll increase the disk space requirements quite a bit and introduces the need for some sort of archiving system, but it’s a possibility.

I’m in immunology/molecular biology. I have a notepad that I use for writing down immediate data and notes, brief procedures, spur-of-the-moment ideas or ideas generated during meetings, and so on. NoteBook is used for “finalizing” things and putting it all into order. The ease with which I can find data compared to my paper-toting labmates is nothing short of incredible. And while I’ve seen some creative solutions for cataloging which reagents are used, nothing can beat downloading MSDS and technical data sheets, placing those PDFs into NoteBook, and then linking to them from corresponding experiment entries. That’d make write the “materials & methods” section of a paper a breeze for anyone, I’d imagine.

Granted, I’m fairly certain that if we were to undergo some sort of audit to determine whether we can use my NoteBook file for patent disputes or something of that sort, it’d likely fail. I make my entries on notepages (rather than writing pages) and bulletpoint furiously, instead of using paragraph mode for each section of an experiment. This affords me lots of “date created/date changed” entries. I’m not sure how that would stand up legally, though… however, most of my labmates seem to have messy paper notebooks as well and I doubt that those could be used either. Not that it’s something to be proud of, but at least mine is organized and has some date logging! :)

By the way, you mentioned a pen that’s resistant to ethanol – is it something that can be used to label centrifuge tubes? If so, would you mind sharing what brand it is? I have yet to find an ethanol-resistant marker, but it’d be pretty helpful…

Import functionality (by Lurch)

Lurch — Mon, 17 Aug 2009 05:40:37 +0000

I’m currently doing a systems engineering masters and have found Notebook a nice tool to have in my arsenal for organising research. However, I am constantly dealing with maths formulas. I’m currently working with MathType for this purpose. It would be handy if I could just import MathType work straight into Notebook like I can into pages. Then if I need to edit work I just double click the work in pages and it opens mathtype.

At present I can cut an past from a MathType document and then paste into notebook(so all is not lost) however, I need to change, I must either redo the work or save the mathtype document and hoepfully remember the file so I can edit i there.

Cheers

Lurch

Requirements for an electronic lab notebook system (commented by Clare )

Clare — Sat, 18 Jul 2009 21:13:36 +0000

The problem I see with electronic notebooks is the fact that things can be changed without leaving a trail of what was replaced.
As a microbiologist, my lab notebook is an almost sacred document. I keep all my methods, notes, ideas, experiments and data in the book. My college professors always emphasized the importance of keeping a well written notebook, including dates, observations and signing each page. Using a waterproof and non-erasable pen is a must. I finally found a pen that won’t disappear if I spill 100% EtOH on my notebook.

The most immediate problem I see with electronic notebooks especially in a life sciences situation is the danger to computers. I would NEVER bring my laptop into our lab. 1. It is a BSL2+ (deadly pathogens) lab. 2. Bench space is tight. 3. So much is going on in the lab, I often have a culture in one hand, a bunsen burner on, agar plates and tubes of media on my bench. It is hard enough trying to keep all the tubes upright. I would never expose my computer to that kind of environment.

Everybody in our lab has a special “lab/dirty” pen to take notes during an experiment and a clean pen for notes at our desks.

Since notebooks are legal documents, it would be important to have a record of things that have been crossed out and a way to ensure that a time stamp can’t be altered.

Requirements for an electronic lab notebook system (commented by Travis)

Travis — Wed, 08 Jul 2009 18:07:46 +0000

1. You can create a basic table via Format->Text->Inline Table. In the future basic math functions will be implemented in an update for tables.

2. I will add a Digital Signature to our list of possible future features.

3. An updated Time Stamp(Date Mark) is on our list, but I will let the software team know there has been another request.

Travis
Circus Ponies Software, Inc.

Suggestions for using Notebook to study for MCAT? (by Clare )

Clare — Sat, 04 Jul 2009 18:14:28 +0000

I’m currently studying for the MCAT and using notebook to store my notes.
I usually make physical note cards first then transfer them to my MCAT notebook.

I like that I can move topics around, something that is very difficult with a paper notebook.

However, I’m new to the Notebook software so any tips would be greatly appreciated. I see that there is a robust law community using Notebook but very few scientists and physicians.

Requirements for an electronic lab notebook system (commented by Sanjay Kapoor)

Sanjay Kapoor — Mon, 01 Jun 2009 14:37:26 +0000

I introduced Notebook in the lab for three Ph.D. Students on trial basis. It seems to works better than paper notebooks but still far away from being an ideal solution.
some of the features that I would like to see in your next update:
1. Tables
2. Digital Signatures
3. Date marks (which can not be changed)

Best,
Sanjay

Bucket sorting (by Goofy)

Goofy — Fri, 15 May 2009 20:35:35 +0000

Did you ever come across a list of items that had to be sorted or grouped according to their “categories” or “descriptions” and wanted to do it a better way than cutting and pasting cells in an Excel spreadsheet or Word table? Note, I am not referring to numeric or alphabetic sorting, which those types of programs do very well.

Here’s a generic example of the problem: You have a random list of fruits and vegetables but you want to get them into their proper “buckets” or categories. In the real world, I have to deal with hundreds of “descriptive statements” that need to be grouped and organized. The defining and adding of categorical attributes to go along with each piece of data becomes a tedious, complex and time consuming effort in a spreadsheet or database.

Here’s what I do with NoteBook:

1. Start with the list on a Note Page in “NoteBook-A”. (Random list of fruits and vegetables) I usually import the data from a converted spreadsheet or word document.

2. Create a new “NoteBook-B” so you have both visible on your desktop.

3. Add Divider and Note Pages as desired according to the “buckets” you need. (Fruits Page, Vegetables Page) You can create these on the fly.

4. From “NoteBook-A” select the cell containing “apple” and drag and drop it to the Fruits Page on “NoteBook-B”. (The “apple” is transferred from “NoteBook-A” to “NoteBook-B”)

5. Go back to “NoteBook-A” and select the cell containing “carrots”, drag it to the Contents Card of “NoteBook-B” and hover over the Vegetables bullet. The Vegetables Page opens. Drop the “carrots” there.

6. Continue back and forth until it’s finished. You can easily do more manipulation and ordering now that you have the right things in the right buckets.

This has saved me so much time and frustration! I hate to admit, I used to print out and cut “flash cards”, sort them into piles, sequence the piles and then tag the item in a spreadsheet for numeric sorting! NoteBook…you guys Rock!

Readability of Lab Background ; Horizontal lines how? (commented by Jayson)

Jayson — Wed, 27 Aug 2008 10:18:08 +0000

quote:
Originally posted by Suman C:
I guess my request still stands on having an opaque background for cells, as Jayson mentions above.

This feature was added in NoteBook 2.0 or 2.1 - you can give any cell an opaque background color today.

quote:
One other thing I hope it addresses: making shrunken images look less dithered. Any screen shots that I had to reduce to about 30% looked very dithered until I turned on anti-aliasing. Even then, printed copies looked a bit blurred.

On the screen NoteBook will do its best to scale images so that they look nice. When printing, NoteBook passes the hi-res version of the image to the printer so that when you Save as PDF and zoom in, say, the image isn't blurry. There have been some issues in 2.1 with printing and hi-res images - please contact support ( http://www.circusponies.com/support ) for assistance with this.[/QUOTE]

quote:
One more thing: I think both Jayson and Elizabeth were guests at some times of the MacVoices and MacJury podcasts by Chuck Joiner. I listen to those fairly regularly, and hope they return to be interviewed, especially after version 3 ships.

We will see :-)

Best,

__jayson

Readability of Lab Background ; Horizontal lines how? (commented by Suman.Chakrabarti@nasa.gov)

Suman.Chakrabarti@nasa.gov — Tue, 26 Aug 2008 16:08:59 +0000

Well, after nearly 4 years, I returned to using Notebook. Wrote a draft technical note of a logistics database import process. This product was very useful.

Once again, although I considered using Lab or Engineering page backgrounds – they look wonderful – I decided to just use the "Notes" template for ease of use. And that I wouldn't have to worry about which bold font to use for readability over the highly colorful background.

This decision worked out fine, and my tech note included over 50 screen shots and more copied files. Notebook is still salutary.

I guess my request still stands on having an opaque background for cells, as Jayson mentions above. I believe he mentioned shipping at the end of August for the new version that can do this. I look forward to it.

One other thing I hope it addresses: making shrunken images look less dithered. Any screen shots that I had to reduce to about 30% looked very dithered until I turned on anti-aliasing. Even then, printed copies looked a bit blurred.

One workaround would be to do the reduction in something like Graphic Converter – perhaps I should remind myself that Notebook isn't a graphics program per se.

One more thing: I think both Jayson and Elizabeth were guests at some times of the MacVoices and MacJury podcasts by Chuck Joiner. I listen to those fairly regularly, and hope they return to be interviewed, especially after version 3 ships.

Requirements for an electronic lab notebook system (commented by Jayson)

Jayson — Sun, 17 Aug 2008 11:23:40 +0000

What is the interest level currently of using NoteBook as an ELN? Would anyone who's interested please contact me at info @ circusponies.com?

Best,

__jayson

Requirements for an electronic lab notebook system (commented by dvirshup)

dvirshup — Sun, 17 Aug 2008 00:21:45 +0000

It looks like enthusiasm for the CP Notebook as an ELN has waned - any chance the developers can give us a hint if they might be working on this for release 3.1?

Indices addition (commented by PennBiologist)

PennBiologist — Thu, 21 Feb 2008 11:36:19 +0000

Have you tried assigning the keyword attribute to your Latin names?

To find out how to do this, go to the Help menu of Notebook (or type command(apple)-?) and type "keyword" in the search field. Follow the directions to assign keywords. You can also simply highlight a word and right-click or control-click and make it a keyword that way. The keywords will show up in the Keywords Index.

I think that should do it for you.

Indices addition (by tomjenkins)

tomjenkins — Mon, 18 Feb 2008 17:32:25 +0000

Hi,

I've only just started using notebook and am already wondering how I managed without it!

I'm a biology student and need to find a way of indexing latin names for plants and animals etc.

I've tried various ways of tagging the words so that they appear in the indices. Highlighting didn't work because there doesn't seem to be a way of sorting the index by the highlighted word, only the first and last word of the cell that the highlighted word appears in. Tried creating a custom keyword like 'latin name' but it only indexed the whole cell.

As latin names usually appear in text in italics, I could easily set all the latin names in italics and then look for any words in italics... if only there was an index page for 'words in italics' like there's one for words that are capitalised.

Would it be possible to create this? Anyone else think this is a good idea, or have any suggestions for how I might go about this in another way?

Cheers.

Requirements for an electronic lab notebook system (commented by jjweimer)

jjweimer — Tue, 04 Dec 2007 13:37:55 +0000

I have just started to search (again) for a suitable type of electronic notebook. The Atrium Research site at
http://www.atriumresearch.com/html/eln.htm
gives a reasonably thorough listing of those that appear to be the top contenders (a few options are missing and a few URLs are now dead). They also have produced a document that analyzes results from a 2006 user survey on the use of ELNs (available for ~$2,000 - OUCH!).

One theme that is now consistently promoted for ELNs is compliance with the Food and Drug Administration’s (FDA) Code of Federal Regulations (CFR) 21 Part 11 regarding electronic records and electronic signatures, electronic entry audit trails.

Another is the ability to share/exchange notebook information, ostensibly by integrating the notebook front end as a client with a separate Web server / database system.

Based on what I have seen so far, Notebook from Circus Ponies would be well-placed in feature/price ratio to offer an ELN. A focus on an ELN having many well-designed features for a limited or targeted market share would seem to be best IMO. Perhaps a "plug-in" framework would be a method to design templates for targeted audiences. Anyway, the general conclusions from the two Sept 2007 presentations on the Amphora site at
http://www.amphora-research.com/news.html
might be helpful in this regard.

I also applaud Circus Ponies for the clarity of the information on their Web site - many of the competitors listed on the Atrium Research site just do not want to provide screenshots or documentation about their products without first collecting a user login.

Finally, alas, since I currently have to work on a WinXX system, Notebook is out of the running as a viable choice. I look forward however to picking up again on this thread once I return to the MacOS (in about a year).