OpenLLM-France/wikimedia huggingface dataset:
# DChip/Installation

Obtain the dChip software and gene information files and store them into a local directory, and double-click the program icon to start dChip. This manual is written in a tutorial style. It is best to explore the functionalities of dChip by following the steps described here sequentially. Paragraphs labeled as “[Analysis example]” may be skipped in first reading. Please cite Li and Wong 2001a if dChip results are used in manuscripts.
dChip is a single executable program running on Windows 2000, under which it is being developed. Presumably it can also run properly on Windows NT/XP, but some functions such as clustering picture zooming and image saving do not work properly on Windows 95/98. The computer memory should be as large as the number of chips (e.g. if there are 100 chips to analyze together, we need > 100M memory), since dChip reads in all CEL data of a group of arrays into the memory. dChip is written in Visual C++ and uses Windows-specific functions for graphic tasks. Victoria Perreau has run dChip on an iBook, using the Connectix Virtual PC Windows 2000 software which costs about $225. When running on the iBook (466 MHz, 320 RAM) it takes about 7 times longer to do the analysis than a PC (1000Mhz Pentium III , 256RAM), i.e. 6 CEL files are normalized in 8 minutes instead of 1.
# DD-WRT/"Flashing" Instructions
## Via user interface

The router is to be connect with a LAN cable to the computer on which the firmware file is already loaded. The LAN cable on the router shall not be plugged into the Wan jack, but into one of the usually several LAN jacks.
After logging in, choose update by uploading the firmware file. The memory of the router does in some cases limits the size of the new firmware. During the update, the old and new firmware are on the router together, which can lead to size problems. Therefore it is recommended to load a small firmware at first and after that to update with the required firmware.

## Database
### Source

The DD-WRT portal provide a router database. This database recommends firmware binaries for every suitable router. However, these binaries are not or hardly maintained and may contain bugs that have been known for a long time.
Until 2010, stable versions were regularly released. After 2010 there are many more updates, but these are only available as beta builds.
You can detect the propper firmware by reading the forums or by trying by yourself of the firmware in the download-center. For this, the router database can be of help in order to determine the sub-location for the appropriate firmware. But remember, that newer is not necessarily better.

### Build subtypes

| Type | Description |
| eko | |
| generic | |
| micro | smallest file size |
| mini | build with small file size suitable for first DD-WRT installation |
| mega | full range of services |
| newd | driver based on the kernel 2.4 |
| newd2 | should not be used |
| nokaid | |
| olsrd | |
| special | |
| std | |
| vint | very old Vintage driver for really early Linksys router from about 15 years ago |
| voip | voice over IP support |
| vpn | support of VPN, respectively OpenVPN |

### Linksys router

| Type | Appropriate firmware | Remarks |
| WRT54G v1.1-v3.1 | OpenVPN: ≤r36410 |
| WRT54G v5/v5.1/v6 | | Flashing instructions WRT54G v5/v5.1/v6 |

## What will brick the router

* Flashing with too large firmware file. See above.
* Flashing with an older revision which is first supported for your router. Compare the router database.
* Flashing if router does not support 2.6 version.

## References

* 1 2 Router-Database
* 1 2 3 4 Everything you need to know!
* ↑ Stable Releases
* 1 2 Beta Downloads
* ↑ Version Features
* ↑ K26 Build Supported Router List
# DChip/Design Experiments
## Designing microarray experiments
### Randomize samples

To minimize experimental variation, it is desirable to have the same person perform all the experiments in the same microarray core facility. However if an experiment involves many samples we have to do them on different days. Arrays generated at different days may have “batch difference”, since different reagents are used to amplify and label the samples. This may be detected by unsupervised clustering. Although “Array list file” can be used to alleviate the situation, it is better to consider such effects before doing experiment. For example, if an experiment compares two conditions with multiple samples in each condition, it is less desirable to have all samples of condition A amplified and hybridized in one day, and all samples of condition B done in another day. In such case even if batch effects happen, we cannot tell since they are mixed with real biological variations that we are interested in. Thus it is more reasonable to consider a balanced design where samples of all conditions are randomly distributed into different sample amplification and hybridization days.

### Replicate samples

Another way to reduce the experimental variation is to have replicate samples. If variations are introduced in an unbiased manner in the experimental or analysis steps after the replication point, averaging the final expression values can better estimate the “expression level” at the replication point (variance of the average is inversely proportional to the number of replicates). Replicates can be done from early point to late point following this rough scale: different individuals (cell line strains), independently grown cell lines (pure strain animals), different tissue sample from the same individual, split tissue samples, split mRNA, split IVT, and scanning one array multiple times. We have observed that replicates at split-IVT level usually agree well in terms of expression values and cluster very tightly. Therefore such replications may not help us to better estimate and reduce the variation introduced before the IVT-splitting point.
The practical choice of the point of replication should suit experimental purpose. For example, when an investigator only has very small amount of RNA, the choices are using double-round amplification (which may have 5' bias) or pooling RNA from different animals in the same litter. Pooling more samples is good as long as the gene expression variation among the pooled animals is expected to be smaller than the gene expression difference among the studied biological conditions, but this choice may be more expensive. Even when the sample amount is enough, the choice exists between whether to process the sample of each animal and hybridize it to a different array, or pool the sample of different animals first and then split the pooled samples into several aliquots, and do IVT and hybridization separately into replicate arrays. This situation is more complex and the answer is probably dependent on specific experiment (the number of replicates, what point to replicate and pool, and the variation of genes at these points).
# DChip/Example Method Description

Example method description using dChip
Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer (www.dchip.org; Li & Wong 2001a). The Invariant Set Normalization method (Li & Wong 2001b) was used to normalize arrays at probe cell level to make them comparable, and the model-based method (Li & Wong 2001b) was used for probe-selection and computing expression values. These expression levels were attached with standard errors as measurement accuracy, which were subsequently used to compute 90% confidence intervals of fold changes in two-sample or two-group comparisons (Li & Wong 2001b). The lower confidence bounds of fold changes were conservative estimate of the real fold changes. Genes with increased or decreased expression after treatments by more than 2 fold (lower confidence bound) were selected for further study.
Hierarchical clustering analysis (Eisen et al. 1998) is used to group genes with same expression pattern. A genes is selected for clustering if (1) its expression values in the 20 samples has coefficient of variation (standard deviation / mean) between 0.5 to 10 (2) it is called “Present” by MAS5 (or GCOS or dChip) software in more than 5 samples. Then the expression values for a gene across the 20 samples are standardized to have mean 0 and standard deviation 1 by linear transformation, and the distance between two genes is defined as 1 - r where r is the standard correlation coefficient between the 20 standardize values of two genes. Two genes with the closest distance are first merged into a super-gene and connected by branches with length representing their distance, and are deleted for future merging. The expression level of the newly formed super-gene is the average of standardized expression levels of the two genes (average-linkage) for each sample. Then the next pair of genes (super-genes) with the smallest distance are chosen to merge and the process is repeated until all genes are merged into one cluster. The dendrogram in Figure ? illustrates the final clustering tree, where genes close to each other have high similarity in their standardized expression values across the 20 samples.
# DD-WRT/"Flashing" instructions/Linksys WRT54G v5/v5.1/v6
## Table of Contents

* Supported devices
* Features
* "Flashing" instructions
** General instructions
** Linksys_WRT54G_v5/v5.1/v6
* References

## WRT54G v5/v5.1/v6

* Download these files to a convenient place.
** vxworks_prep_v03.zip
** vximgtoolgui.zip - this is used to generate a vxworkskiller image with your MAC Address embedded.
** dd-wrt.v23_sp2_micro.zip - DD-WRT v23 micro package. The micro package is used because of the little flash memory contained in these routers.
** tftp.exe - graphical TFTP transfer tool
# DD-WRT/Features
## Table of Contents

* Supported devices
* Features
* "Flashing" instructions
** General instructions
** Linksys_WRT54G_v5/v5.1/v6
* References

## Features

These are the features available in the Standard version of DD-WRT. Other versions, such as the Micro or Mini, may lack some specific features to lower the package size.
This list uses content from the WRT Wiki article "What is DD-WRT" as retrieved on September 24, 2006, which is licensed under the GNU Free Documentation License 1.2. This article is in turn, as with all Wikibooks articles are licensed under the GNU Free Documentation License 1.2.
   * 13 languages
   * 802.1x (EAP (Extensible Authentication Protocol) encapsulation over LANs)
   * Access Restrictions
   * Adhoc Mode
   * Afterburner
   * Client Isolation Mode
   * Client Mode (supports multiple connected clients)
   * Client Mode WPA
   * DHCP Forwarder (udhcp)
   * DHCP Server (udhcp or Dnsmasq)
   * DNS forwarder (Dnsmasq)
   * DMZ
   * Dynamic DNS (DynDNS, easyDNS, FreeDNS, No-IP, TZO, ZoneEdit, custom, and others)
   * Hotspot Portal (Sputnik Agent ,Chillispot)
   * IPv6 Support
   * JFFS2
   * MMC/SD Card Support (hardware modification required)
   * NTP client in a client-server basis
   * Ntop Remote Statistic
   * OpenVPN Client & Server (only in -vpn build of the firmware)
   * Port Triggering
   * Port Forwarding (max. 30 entries)
   * PPTP VPN Server & Client
   * QoS Bandwidth Management (Optimize for Gaming and Services / Netmask / MAC / Ethernet Port Priority)
   * QoS L7 Packet Classifier l7-filter)
   * RFlow/MACupd
   * Routing: Static entries and Gateway, BGP, OSPF & RIP2 via (BIRD)
   * Samba FS Automount
   * Syslog to remote server
   * Rx/Tx Antenna (Select or Auto)
   * Show Status of Wireless Clients and WDS with System Uptime/Processor Utilization
   * Site Survey
   * SNMP
   * SSH server & client (dropbear)
   * Startup, Firewall, and Shutdown scripts (startup script)
   * Static DHCP Assignment
   * Style (Changeable GUI; v.23)
   * Supports New Devices (WRT54G V3, V3.1, V4, V5 and WRT54GS V2.1, V3, V4)
   * Telnet server & client
   * Transmit Power Adjustment (0-251mW, default is 28mW, 100mW is safe)
   * UPnP
   * VLAN
   * Wake On Lan client (WOL)
   * WDS Connection Watchdog
   * WDS Repeater Mode
   * Wireless MAC Addresses Cloning
   * Wireless MAC filter
   * WMM (Wi-Fi MultiMedia QoS)
   * WPA over WDS
   * WPA/TKIP with AES
   * WPA2
   * Xbox Kaid (Kai Engine)
# DD-WRT

DD-WRT is an alternate firmware available for Wi-Fi routers. This software is usually not officially supported by the original manufacturer of the router and the use may void your warranty. DD-WRT is free, open source software licensed under the GNU General Public License version 2. The official website is http://www.dd-wrt.com/.

## Table of Contents

* Features
* Supported devices
* Flashing
* User interface
* References

## Motivation

This book is intended to give a compact overview of the possibilities and usage of DD-WRT, especially for users who are not primarily concerned with the topic of routers. Therefore, it can not and shall not replace the wiki and the forum of the official website, which provide a high amount of detailed information.
In some fields requires router software specific background knowledge, so that it is not always possible to avoid using technical terms. If possible and requirded, these should be shortly explained here.
Anyone can contribute to this book.
# Basic Book Design/Introduction
## How to help with this book

I wrote "Basic Book Design" using Microsoft Word. I don't have time to reformat it as a wikibook but I welcome anyone who volunteers to do that. You can download my MS Word file from my website. The file is 1.9MB. Pick a chapter you want to work on, pull it from the MS Word file, put it into the wikibook and clean up the formatting.--Thomas David Kehoe 03:09, 7 September 2006 (UTC)

## Who is this book for

This book is for those wishing to learn about Basic Book Design. It is pitched at an American audience. Many elements of book design - typesetting, copyediting, etc. - are different in North America from the rest of the English-speaking world, so this book may not be suitable for non-American readers.

## Traditional Rules vs. "Keep Out Of Trouble" Rules

Often in this book you'll see two, or even three, rules regarding an issue. For the traditional rules of book design, we refer to the Chicago Manual of Style. When we refer to such a rule, we list the chapter and paragraph number from the Chicago Manual of Style (e.g., 12.34), so you can look up the rule. (We're using the 14th edition.)
We also explain what word processors — in particular Microsoft Word — do. Sometimes word processors follow rules different from traditional rules. And often we present novice or "keep out of trouble" rules. These are rules that novices should follow to avoid making awful, obvious, knock 'em dead mistakes. And, usually, the Chicago Manual of Style lists 14 pages of exceptions to our rule. Professional book designers shouldn't follow our "keep out of trouble" rules.
The rules for choosing between the rules is, if you understand the traditional rules, follow them. If you don't understand the traditional rules, follow our "keep out of trouble" rules.
If you follow our "keep out of trouble" rules, 99.9% of your readers won't notice that you didn't follow traditional rules. Many of the traditional rules are arcane, and known only by book industry professionals. But remember that you may have to "sell" your book to key book industry professionals — e.g., book reviewers — who'll notice amateur typesetting.
In a few places we'll suggest new ideas that we thought of. These aren't rules.
# Basic Book Design/Indentation

Don't indent the ﬁrst paragraph of a chapter or section. Only following paragraphs are indented.
    LaTeX automatically does this. Microsoft Word doesn’t.
    If you use Microsoft Word, you'll have to create a new style for "First Paragraph" and manually set all these ﬁrst paragraphs into that style.

## How Much To Indent?

If you choose to indent paragraphs (as opposed to setting them with a small space between each), set your indentation in as far as the font is high. E.g., if you’re using a 12-pt font, indent your paragraphs about 12 points, or 0.17 inches. Visually, 12-pt Helvetica is quite different than 12-pt Times New Roman, so you might want to make adjustments based on the visual appearance.
Indent no more than the leading (space between lines within a paragraph). E.g., with 15-pts leading, indent no more than 15-pts indentation, or 0.21 inches.
Microsoft Word's default indentation is set to 0.5 inches. This comes from the days of creating a manuscript on a monospaced typewriter (five spaces was about one-half inch) and from the half-inch automatic tab stops made popular by the first word processing software.
Spacing between paragraphs is a related consideration. If you choose the more modern digital design of having space denote a paragraph break, then paragraph indentation is overkill—unless you want it for design aesthetics. Indentation exists because it was cheaper for early printers to do that than to add strips of lead between paragraphs, thus increasing the total number of pages required per book and increasing costs per unit. As a design element, indentation raises questions, such as the questionable need for indentation of running dialogue.
As e-reader devices overtake paper book sales, book design aesthetics will evolve as well. There is little reason to maintain the printer’s status quo when there is no longer a printer involved. As with all good design, use common sense, have a reason for your choices, keep things consistent, and don't be afraid to break a few so-called rules.
# Basic Book Design/Justification
## Keep Out Of Trouble Rules

Use justified paragraphs.
Justiﬁed text has even left and right margins. Unjustiﬁed text has an even left margin and a "ragged right" margin.
| This paragraph is justiﬁed. This sentence is in a justiﬁed paragraph. This sentence is also in a justiﬁed paragraph. This sentence is—you guessed it!—also in a justiﬁed paragraph. | This paragraph is ragged right. This sen-tence is in a ragged right paragraph. This sentence is also in a ragged right para-graph. This sentence is—you guessed it!—also in a ragged right paragraph. |
Typeset books use justiﬁed text. Justified text looks nicer. Readers are used to reading justiﬁed text, so justiﬁed text is easier to read.
"Ragged right" text improves retention. I.e., if you want readers to remember what you wrote, and especially to return and ﬁnd items they'd read earlier, use of "ragged right" may be justified (sorry, I couldn't resist the pun). Just as readers recognize words by their shape, they also remember ideas by the shape of the paragraph.
"Ragged right" text should be used in one other situation. If the column is very narrow, or the font size is very big, or the words are very long (e.g., website URLs), justified text can produce huge white spaces between words, called open lines. Open lines are a sign of amateur typesetting.
Instead, set a website URL centered on its own line. If you're forced to use a narrow column (e.g., ﬂowing text around an illustra-tion), look at it both justiﬁed and "ragged right," and choose what looks best.
Text is always justiﬁed by increasing white space between words, never between letters within words. The latter (called letterspacing) would make word shapes difﬁcult to recognize. Text should always be justified by adding equal amounts of space between all words on a line. Early word processors (in the 1980s) put two spaces between some words and one space between other words. That looked awful.
# Basic Book Design/Master Documents

If your computer is slow, use master documents. Most word processors can make each chapter a separate chapter, then join them together as a book. Moving between chapters will be slower, but saving, typing, etc. will be faster.
I’ve never used Microsoft Word in master document mode. Several people have told me that it's a "bug-ridden monstrosity." If this is true, and you need to make master documents, consider another software application, e.g., Adobe InDesign.
# Basic Book Design/Me, Myself and I

Avoid mentioning yourself when writing. We naturally talk about ourselves in conversation, so it's easy to write this way. But it doesn't sound professional.
Use Find to search for "I" and "me". Rewrite the sentences without mentioning yourself. Or take out the material—it probably doesn't add anything.
Using the phrase "the author" sounds stuffy.
Avoid telling personal stories. Stories take up more room than simply stating the point.
Like unusual fonts, break this rule if you have a good reason. E.g., your book is a memoir, or a book of personal essays.
# Basic Book Design/Leading
## Keep Out of Trouble Rules

* When using book-length lines (65-70 characters per line, including spaces), don't use single-spaced or double-spaced settings. Instead, use "At Least" settings.
* When using book-length lines, use two or three points of leading, e.g., 15 points leading with a 12-point font.
* When using wider lines, e.g., in a letter, use wider leading. Use double-spacing or one-and-a-half spacing.

## Definitions

leading solid

### Leading

Leading (pronounced like lead, the metal, not lead, what your dog does when walking you) is the space between lines of text. It's also called spacing, as in single-spaced, double-spaced, etc.
Fonts and leading are referred to as two numbers. E.g., "12/13" or "12 on 13 points" is a 12-point font with 13 points of leading.

### Solid

Single-spaced can be the same as the font size (called solid), e.g., a 12-point font on 12-point leading. Or it can be the font size plus one point, e.g., a 12-point font on 13 points of leading is single-spaced. Check what your word processor does.
A 12-point font with one-and-a-half spacing is 18 points of leading, or 12/18.
A 12-point font with double spacing is 24 points of leading, or 12/24. Use two or three points of leading. E.g., 11/13, or 12/15. This is easier to read than single-spaced (one point of leading).
More than three points of leading is usually unnecessary. Your book will be longer, increasing printing costs. Readers will have to move their eyes more, and turn more pages.
# Basic Book Design/Page Size
## Basic Book Design Rules

* For books printed on offset printers, use a 6"x 9" (152mm x 229mm) page size.
* For books or anything else printed on laser printers (including Xerox Docutech printers), use 5.5"x8.5" (140mm x 216mm) or 8.5"x11" (216mm x 280mm) page size mf.
The standard book size is six inches wide and nine inches tall (6"x 9"). Your book will probably be cheapest to print, easiest to read, and easiest to sell (e.g., it'll fit on bookstore shelves) in this size.
Larger books are harder to hold, carry, or put on a shelf.
Smaller books lose disproportionately more space to margins, increasing the cost. A 6"x 9" book has nearly 20% more text space. But a 6"x 9" book costs only about 5% more than a 5.5" x 8.5" book. The result is a 15% cost savings.
The cover of a 6"x 9" book is 15% larger than a 5.5"x8.5" book. The cover is your best advertising space. In a bookstore window, passersby are more likely to see a larger book.
Setting up your software applications for 6"x 9" pages can be tricky. In Microsoft Word, go the File…Page Setup…Settings… Custom Paper Size.

### Inkjet Printer Limitations

If you have an inkjet printer connected to your computer, Microsoft Word usually won't allow a 0.5" (12.7mm) bottom margin. Depending on the printer, it may require a minimum 0.56" (14.2mm) or 0.67" (17mm) bottom margin. 0.06 (1.5mm) inches may not sound like much, but in a 224-page book, that's two extra pages.
Most newer computers and laptops can have no margin at all (using google docs.. etc), but if you are using old software, to get around this limitation, tell Microsoft Word you're using a laser printer. Word should then allow a bottom margin up to 0.2".
Alternatively, use the default paper size, e.g., 8.5"x11". Save your document as a PDF file, and use Adobe Acrobat to crop the pages.