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Frequently Asked Questions About The Scriptome

What? Vocabulary questions

What's the Scriptome?

The Scriptome is a toolbox helping biologists explore and manipulate their data. For more information, see the Overview page.

What's an atom?

An atom is a single Scriptome tool. It's called an atom because it does one, small thing. Also, because atoms can be combined to make molecules (which we, breaking our analogy completely, call protocols). Atoms can be found in the Tools section of the navigation bar on the left.

What's a protocol?

A protocol is an ordered set of Scriptome atoms which can solve a larger problem. The analogy is to a biological protocol (such as those at, which is an ordered set of actions that solve a larger biological problem. Protocols can be found in the Protocols section of the navigation bar on the left, although users will often want to build their own protocols.

How? Usage questions

How do I download and install the Scriptome?

You don't! You just cut and paste. Windows users without access to a UNIX or Mac will need to download Perl (free, one-click install) from

How do I use the Scriptome?

First, choose whether you want the Windows or non-Windows tools. Find the right tool, change parameters and filenames in the form as desired, cut and paste the text in the colored box onto a Windows, UNIX, or Mac command line, and hit Enter. For more information, see the Help page.

How do the tools work?

Each tool is a command that runs Perl. Rather than running Perl programs (like "perl infile > outfile"), we use the -e option to write a short Perl program right on the command line, also known as a "Perl one-liner". So each tool is usually in the form perl -e 'Perl code' infile(s) > outfile The '>' sends the output from running the Perl code on the input file(s) to the given outfile instead of the screen.

How do I run the tools on Windows / UNIX / Mac / Linux?

Choose the Windows site when you first start, or use the links in the very top left of the page to switch between Unix/Mac and Windows. (Linux and Mac count as UNIX.) This will change the color of the navigation bar and the light backgrounds for the code you cut and paste. UNIX is blue, Windows is green.

How do I join the mailing lists (or see the archives)?

See the information on the different Scriptome mailing lists.

How do I submit a bug report?

Bug reports and other feedback options are described on the Resources page.

How can I request a new Scriptome tool or protocol?

Send email to with a detailed request. We won't guarantee that we'll create it, but if several people ask for similar things, we're more likely to create them. You might also want to discuss it on the mailing list.

How can I submit a new Scriptome tool or protocol?

Send email to including code, sample input and output files, and clear, concise documentation.

Why? Design questions

Why is the Scriptome necessary?

It's frustrating for programmers to see non-programming biologists spending hours to edit files by hand (or even abandoning certain avenues of analysis), when a short program can do the work in a few seconds. Yet more and more questions require high-throughput analysis that makes some programming necessary. (The Scriptome can also be viewed as a repository of frequently requested scripts, so that we don't have to write the same script each time a different biologist asks for it.)

Why is the Scriptome built the way it is?

See the Principles page for more information on why certain design decisions were made (including hints to many questions below).

The Scriptome project is essentially a project to give non-programmers some of the power of programming, without forcing them to learn a (classic) programming language. This is a field of current research in computer science, and we're hoping to use (steal) some computer scientists' ideas on how to do this more effectively in the future.

Why do the tools use ugly text instead of a graphical interface (point and click)?

Any interface, no matter how "intuitive", is another interface users need to learn. Since users may be using the Scriptome only occasionally, why not just use cut-and-paste? Also, given that we may need to write many tools to solve diverse and evolving needs, a text/web interface allows much faster tool development. Finally, the current interface requires no downloads or installs, and is generally platform- and browser-independent. That said, these tools are simple enough that they can be wrapped inside graphical tools. We're working on some ideas....

Why not just make biologists learn programming?

We're all for it! However, many biologists - especially those who need to use computers for analysis only occasionally - do not consider it worth the time to learn programming. Alternatively, the Scriptome can be viewed as a first step towards programming: it can help biologists learn about problem decomposition, high-throughput analysis, and debugging, while avoiding the additional barrier of learning syntax and other programming techniques (variables, arrays, hashes, regular expressions...); and it provides short, working examples for student programmers to read and tweak.

Why not just make biologists learn UNIX?

Yes, many of these tools can be implemented with UNIX tools like grep, cut, paste, join, awk, sed.... However: UNIX tools tend to give "concise" feedback; they tend to have many, many options; and shell scripting can be even more cryptic than Perl. It's possible to imagine a Scriptome with cut-and-paste pure UNIX commands instead of Perl, which would get around some of these problems. But using Perl means we can also write biology-specific tools pretty easily (possibly stealing them from Bioperl).

Why not just make biologists learn Excel/Access?

Many biologists do use Excel, but they might not use fancy functions or macros. The interface may not work for occasional users, or they may feel that learning an "advanced" program like Access is a waste of time. And while Excel and Access can do many of the jobs the Scriptome does, they are not designed to handle FASTA formats, for example. (Excel 2003 will also choke on files with more than 65535 rows, and won't merge files without VB programming.)

Why Perl?

Perl was specifically designed for "data munging" - formatting, filtering, etc. - which is why it's so commonly used for bioinformatics. It was also designed to allow fast code development, which is important given the diverse and changing questions biologists will be asking. We can take advantage of existing tools, most obviously Bioperl. And Perl is automatically available on every UNIX/Mac computer, so no install is needed.

Why separate tools for Windows?

The Windows command line expects you to say perl -e "blah" while the UNIX shell expects perl -e 'blah'. So we have to change single quotes to double. But then any double quotes within the script would confuse Windows, so, e.g., instead of print "blah" we use the more mystical print qq~blah~.

Boring and annoying, but necessary.

Who? Credit questions

Who wrote the Scriptome?

The Scriptome was developed by the Computational Biology Group at Harvard University's Bauer Center for Genomics Research. (Follow links at the top of the page.)

  • Amir Karger is the main developer.

  • Jason Konrad is a non-biologist working on the Perl side of the Scriptome.

  • Eitan Rubin, who provided many ideas about the principles is now at Ben Gurion University, working on embedding the Scriptome in Excel.

  • Chris Botka, who provided initial ideas for the Scriptome, is now at the Joslin Diabetes Center.

  • Professor Rob Miller at MIT provided many user interface improvements.

  • Many others provided ideas for tools or protocols.

We hope to have a real credits page someday.

Whom do I send my money to?

Believe it or not, we're providing these tools for you absolutely free! On the other hand, if you have some money available to fund objectives like ours (creating tools for non-programming scientists, giving non-programmers some of the power of programming), send an email to

Where? Future questions

Where is the Scriptome headed?

We have several zillion ideas. We might decide to change the interface if too many biologists dislike the command line. There are plenty of tools and protocols to write. We would like to add an "explain this" button to each tool, so that Perl students can get a detailed explanation of how the tools work.


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